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Sample records for accurate quantum chemical

  1. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  2. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    SciTech Connect

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.

  3. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  4. Toward an Accurate Estimate of the Exfoliation Energy of Black Phosphorus: A Periodic Quantum Chemical Approach.

    PubMed

    Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti

    2016-01-01

    The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems. PMID:26651397

  5. Toward an Accurate Estimate of the Exfoliation Energy of Black Phosphorus: A Periodic Quantum Chemical Approach.

    PubMed

    Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti

    2016-01-01

    The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems.

  6. How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.

    SciTech Connect

    Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.

    2003-03-01

    Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

  7. Quantum chemical approach for condensed-phase thermochemistry (III): Accurate evaluation of proton hydration energy and standard hydrogen electrode potential

    NASA Astrophysics Data System (ADS)

    Ishikawa, Atsushi; Nakai, Hiromi

    2016-04-01

    Gibbs free energy of hydration of a proton and standard hydrogen electrode potential were evaluated using high-level quantum chemical calculations. The solvent effect was included using the cluster-continuum model, which treated short-range effects by quantum chemical calculations of proton-water complexes, and the long-range effects by a conductor-like polarizable continuum model. The harmonic solvation model (HSM) was employed to estimate enthalpy and entropy contributions due to nuclear motions of the clusters by including the cavity-cluster interactions. Compared to the commonly used ideal gas model, HSM treatment significantly improved the contribution of entropy, showing a systematic convergence toward the experimental data.

  8. Accurate Characterization of the Peptide Linkage in the Gas Phase: A Joint Quantum-Chemical and Rotational Spectroscopy Study of the Glycine Dipeptide Analogue.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Largo, Laura; Peña, Isabel; Cabezas, Carlos; Alonso, José Luis

    2014-02-01

    Accurate structures of aminoacids in the gas phase have been obtained by joint microwave and quantum-chemical investigations. However, the structure and conformational behavior of α-aminoacids once incorporated into peptide chains are completely different and have not yet been characterized with the same accuracy. To fill this gap, we present here an accurate characterization of the simplest dipeptide analogue (N-acetyl-glycinamide) involving peptidic bonds. State-of-the-art quantum-chemical computations are complemented by a comprehensive study of the rotational spectrum using a combination of Fourier transform microwave spectroscopy with laser ablation. The coexistence of the C7 and C5 conformers has been proved and energetically as well as spectroscopically characterized. This joint theoretical-experimental investigation demonstrated the feasibility of obtaining accurate structures for flexible small biomolecules, thus paving the route to the elucidation of the inherent behavior of peptides.

  9. Quantum Chemical Calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Arnold, James O. (Technical Monitor)

    1997-01-01

    The current methods of quantum chemical calculations will be reviewed. The accent will be on the accuracy that can be achieved with these methods. The basis set requirements and computer resources for the various methods will be discussed. The utility of the methods will be illustrated with some examples, which include the calculation of accurate bond energies for SiF$_n$ and SiF$_n^+$ and the modeling of chemical data storage.

  10. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  11. Highly Accurate Quantum-Chemical Calculations for the Interstellar Molecules C_3 and l-C_3H^+

    NASA Astrophysics Data System (ADS)

    Botschwina, Peter; Schröder, Benjamin; Stein, Christopher; Sebald, Peter; Oswald, Rainer

    2014-06-01

    Composite potential energy surfaces with coupled-cluster contributions up to CCSDTQP were constructed for C_3 and l-C_3H^+ and used in the calculation of spectroscopic properties. The use of very large AO basis sets and the consideration of higher-order correlation beyond CCSD(T) is of utmost importance for C_3 in order to arrive at quantitative spectroscopic data. The first detection of l-C_3H^+ in the interstellar medium was reported by Pety et al., who attributed 9 radio lines observed in the horsehead photodissociation region to that species. That assignment was questioned by the recent theoretical work of Huang et al. However, our more accurate calculations are well in support of the original assignment. The calculated ground-state rotational constant is B_0 = 11248 MHz, only 0.03% off from the radio astronomical value of 11244.9512±0.0015 MHz. The ratio of centrifugal distortion constants D_0(exp.)/D_e(theor.) of 1.8 is quite large, but reasonable in comparison with C_3O and C_3. J. Pety, P. Gratier, V. Guzmán, E. Roueff, M. Gerin et al., Astron. Astrophys. 2012, A68, 1-8. X. Huang, R. C. Fortenberry, T. J. Lee, Astrophys. J. Lett. 2013, 768:L25, 1-5. P. Botschwina, R. Oswald, J. Chem. Phys. 2008, 129, 044305

  12. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State 17O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds

    PubMed Central

    Rorick, Amber; Michael, Matthew A.; Yang, Liu; Zhang, Yong

    2015-01-01

    Oxygen is an important element in most biologically significant molecules and experimental solid-state 17O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state 17O NMR chemical shift tensor properties are still challenging in many cases and in particular each of the prior computational work is basically limited to one type of oxygen-containing systems. This work provides the first systematic study of the effects of geometry refinement, method and basis sets for metal and non-metal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups, X= H, C, N, P, and metal. The experimental range studied is of 1455 ppm, a major part of the reported 17O NMR chemical shifts in organic and organometallic compounds. A number of computational factors towards relatively general and accurate predictions of 17O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied various kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient R2 of 0.9880 and mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and R2 of 0.9926 for all shift tensor properties. These results shall facilitate future computational studies of 17O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help refinement and determination of active-site structures of some oxygen-containing substrate bound proteins. PMID:26274812

  13. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

    PubMed

    Rorick, Amber; Michael, Matthew A; Yang, Liu; Zhang, Yong

    2015-09-01

    Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

  14. The calculation of accurate 17O hyperfine coupling constants in the hydroxyl radical: A difficult problem for current quantum chemical methods

    NASA Astrophysics Data System (ADS)

    Wetmore, Stacey D.; Eriksson, Leif A.; Boyd, Russell J.

    1998-12-01

    The hyperfine coupling constants (HFCCs) in the hydroxyl radical are investigated through comparison of results obtained from a variety of quantum chemical methods. The couplings obtained from the multi-reference configuration interaction (MRCI) wave function, built upon the restricted open-shell Hartree-Fock (ROHF) reference determinant, are investigated in terms of the basis set, the configuration selection energy threshold, and the size of the reference space. Overall results which converge to the experimental couplings are obtained for hydrogen, but not for oxygen. In particular, the MRCI method shows no improvement over density functional theory (the B3LYP functional), for the calculation of Aiso(17O). On the other hand, results in excellent agreement with experiment are obtained through the use of the quadratic configuration interaction (QCISD) method based on the unrestricted HF (UHF) reference determinant with the identical basis sets. Examination of UHF and ROHF based coupled-cluster methods, CCSD and CCSD(T), indicates that once a high enough level of electron correlation is included, the oxygen HFCC is independent of the form of the reference determinant. Unlike the ROHF-CCSD method, which yields reliable results once the effects of triple excitations have been taken into account, the MRCI wave function cannot easily be adjusted to account for the inadequacies of the ROHF reference determinant in order to accurately predict 17O HFCCs.

  15. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    PubMed

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  16. Beyond transition state theory: accurate description of nuclear quantum effects on the rate and equilibrium constants of chemical reactions using Feynman path integrals.

    PubMed

    Vanícek, Jirí

    2011-01-01

    Nuclear tunneling and other nuclear quantum effects have been shown to play a significant role in molecules as large as enzymes even at physiological temperatures. I discuss how these quantum phenomena can be accounted for rigorously using Feynman path integrals in calculations of the equilibrium and kinetic isotope effects as well as of the temperature dependence of the rate constant. Because these calculations are extremely computationally demanding, special attention is devoted to increasing the computational efficiency by orders of magnitude by employing efficient path integral estimators.

  17. Efficient and accurate modelling of quantum nanostructures

    NASA Astrophysics Data System (ADS)

    Ayad, Marina; Obayya, Salah S. A.; Swillam, Mohamed A.

    2016-03-01

    An efficient sensitivity analysis approach for quantum nanostructures is proposed. The imaginary time propagation method (ITP) is utilized to solve the Time Dependent Schrödinger's Equation (TDSE). Using this method, an extraction of all the modes and their sensitivity with respect to all the design parameters have been performed with minimal computational effort. The sensitivity analysis is performed using the Adjoint Variable Method (AVM) and results are comparable to those obtained using Central Finite Difference Method (CFD) applied directly on the response level.

  18. Quantum Entanglement and Chemical Reactivity.

    PubMed

    Molina-Espíritu, M; Esquivel, R O; López-Rosa, S; Dehesa, J S

    2015-11-10

    The water molecule and a hydrogenic abstraction reaction are used to explore in detail some quantum entanglement features of chemical interest. We illustrate that the energetic and quantum-information approaches are necessary for a full understanding of both the geometry of the quantum probability density of molecular systems and the evolution of a chemical reaction. The energy and entanglement hypersurfaces and contour maps of these two models show different phenomena. The energy ones reveal the well-known stable geometry of the models, whereas the entanglement ones grasp the chemical capability to transform from one state system to a new one. In the water molecule the chemical reactivity is witnessed through quantum entanglement as a local minimum indicating the bond cleavage in the dissociation process of the molecule. Finally, quantum entanglement is also useful as a chemical reactivity descriptor by detecting the transition state along the intrinsic reaction path in the hypersurface of the hydrogenic abstraction reaction corresponding to a maximally entangled state.

  19. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    PubMed

    Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

    2014-03-11

    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

  20. An accurate and simple quantum model for liquid water.

    PubMed

    Paesani, Francesco; Zhang, Wei; Case, David A; Cheatham, Thomas E; Voth, Gregory A

    2006-11-14

    The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics

  1. Accurate fluorescence quantum yield determination by fluorescence correlation spectroscopy.

    PubMed

    Kempe, Daryan; Schöne, Antonie; Fitter, Jörg; Gabba, Matteo

    2015-04-01

    Here, we present a comparative method for the accurate determination of fluorescence quantum yields (QYs) by fluorescence correlation spectroscopy. By exploiting the high sensitivity of single-molecule spectroscopy, we obtain the QYs of samples in the microliter range and at (sub)nanomolar concentrations. Additionally, in combination with fluorescence lifetime measurements, our method allows the quantification of both static and collisional quenching constants. Thus, besides being simple and fast, our method opens up the possibility to photophysically characterize labeled biomolecules under application-relevant conditions and with low sample consumption, which is often important in single-molecule studies.

  2. Quantum mechanical calculations to chemical accuracy

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1991-01-01

    The accuracy of current molecular-structure calculations is illustrated with examples of quantum mechanical solutions for chemical problems. Two approaches are considered: (1) the coupled-cluster singles and doubles (CCSD) with a perturbational estimate of the contribution of connected triple excitations, or CCDS(T); and (2) the multireference configuration-interaction (MRCI) approach to the correlation problem. The MRCI approach gains greater applicability by means of size-extensive modifications such as the averaged-coupled pair functional approach. The examples of solutions to chemical problems include those for C-H bond energies, the vibrational frequencies of O3, identifying the ground state of Al2 and Si2, and the Lewis-Rayleigh afterglow and the Hermann IR system of N2. Accurate molecular-wave functions can be derived from a combination of basis-set saturation studies and full configuration-interaction calculations.

  3. Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions

    SciTech Connect

    Gray, S.K.

    1993-12-01

    A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.

  4. Quantum instanton approximation for thermal rate constants of chemical reactions

    NASA Astrophysics Data System (ADS)

    Miller, William H.; Zhao, Yi; Ceotto, Michele; Yang, Sandy

    2003-07-01

    A quantum mechanical theory for chemical reaction rates is presented which is modeled after the [semiclassical (SC)] instanton approximation. It incorporates the desirable aspects of the instanton picture, which involves only properties of the (SC approximation to the) Boltzmann operator, but corrects its quantitative deficiencies by replacing the SC approximation for the Boltzmann operator by the quantum Boltzmann operator, exp(-βĤ). Since a calculation of the quantum Boltzmann operator is feasible for quite complex molecular systems (by Monte Carlo path integral methods), having an accurate rate theory that involves only the Boltzmann operator could be quite useful. The application of this quantum instanton approximation to several one- and two-dimensional model problems illustrates its potential; e.g., it is able to describe thermal rate constants accurately (˜10-20% error) from high to low temperatures deep in the tunneling regime, and applies equally well to asymmetric and symmetric potentials.

  5. ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS

    PubMed Central

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-01-01

    The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multi-finite buffers for reducing the state space by O(n!), exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes, and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be pre-computed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multi-scale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks. PMID:27761104

  6. How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

    PubMed

    Grima, Ramon; Thomas, Philipp; Straube, Arthur V

    2011-08-28

    The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remains to be clarified. We use the system-size expansion to show that chemical Fokker-Planck estimates of the mean concentrations and of the variance of the concentration fluctuations about the mean are accurate to order Ω(-3∕2) for reaction systems which do not obey detailed balance and at least accurate to order Ω(-2) for systems obeying detailed balance, where Ω is the characteristic size of the system. Hence, the chemical Fokker-Planck equation turns out to be more accurate than the linear-noise approximation of the chemical master equation (the linear Fokker-Planck equation) which leads to mean concentration estimates accurate to order Ω(-1∕2) and variance estimates accurate to order Ω(-3∕2). This higher accuracy is particularly conspicuous for chemical systems realized in small volumes such as biochemical reactions inside cells. A formula is also obtained for the approximate size of the relative errors in the concentration and variance predictions of the chemical Fokker-Planck equation, where the relative error is defined as the difference between the predictions of the chemical Fokker-Planck equation and the master equation divided by the prediction of the master equation. For dimerization and enzyme-catalyzed reactions, the errors are typically less than few percent even when the steady-state is characterized by merely few tens of molecules.

  7. Chemical accuracy from quantum Monte Carlo for the benzene dimer.

    PubMed

    Azadi, Sam; Cohen, R E

    2015-09-14

    We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is -2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods. PMID:26374029

  8. Chemical accuracy from quantum Monte Carlo for the benzene dimer

    SciTech Connect

    Azadi, Sam; Cohen, R. E.

    2015-09-14

    We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of −2.3(4) and −2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is −2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

  9. Chemical accuracy from quantum Monte Carlo for the benzene dimer.

    PubMed

    Azadi, Sam; Cohen, R E

    2015-09-14

    We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is -2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

  10. Quantum chemical studies of estrogenic compounds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

  11. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

    PubMed Central

    Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

  12. An accurate, efficient algorithm for calculation of quantum transport in extended structures

    SciTech Connect

    Godin, T.J.; Haydock, R.

    1994-05-01

    In device structures with dimensions comparable to carrier inelastic scattering lengths, the quantum nature of carriers will cause interference effects that cannot be modeled by conventional techniques. The basic equations that govern these ``quantum`` circuit elements present significant numerical challenges. The authors describe the block recursion method, an accurate, efficient method for solving the quantum circuit problem. They demonstrate this method by modeling dirty inversion layers.

  13. Sensitive chemical compass assisted by quantum criticality

    NASA Astrophysics Data System (ADS)

    Cai, C. Y.; Ai, Qing; Quan, H. T.; Sun, C. P.

    2012-02-01

    A radical-pair-based chemical reaction might be used by birds for navigation via the geomagnetic direction. The inherent physical mechanism is that the quantum coherent transition from a singlet state to triplet states of the radical pair could respond to a weak magnetic field and be sensitive to the direction of such a field; this then results in different photopigments to be sensed by the avian eyes. Here, we propose a quantum bionic setup, inspired by the avian compass, as an ultrasensitive probe of a weak magnetic field based on the quantum phase transition of the environments of the two electrons in the radical pair. We prove that the yield of the chemical products via recombination from the singlet state is determined by the Loschmidt echo of the environments with interacting nuclear spins. Thus quantum criticality of environments could enhance the sensitivity of detection of weak magnetic fields.

  14. Remote Chemical Detection using Quantum Cascade Lasers

    SciTech Connect

    Hatchell, Brian K.; Harper, Warren W.; Gervais, Kevin L.

    2006-02-01

    The Infrared Technologies Program at the Pacific Northwest National Laboratory (PNNL) is focused on the science and technology of remote and in-situ chemical sensors for detecting proliferation and countering terrorism. The program is focusing on the infrared detection of gaseous species including chemical warfare agents and gases associated with the production of chemical and nuclear weapons. Several sensors under development are based on miniature infrared quantum cascade (QC) lasers constructed of semiconductor material. The QC laser is unique in that by simply changing the thickness of the semiconductor layers, the laser's wavelength can be changed to target molecular absorption features of specific chemicals. For remote sensing over long optical paths, QC lasers are applied to remote areas using the differential-absorption LIDAR technique. Using a single laser, this technique can easily monitor large areas that would require a large network of point sensors. The original remote sensing configuration, suitable for laboratory applications, consisted of an optical table, laser, beam expander, telescope, mirror, and various supporting electronic and optical components. Recently, PNNL began development of a ruggedized version to conduct experiments in real-world conditions. To reduce the effects of thermal distortion, the system had to be operated from within a large, well insulated, temperature-controlled trailer. The optical breadboard was attached to 4 shock-mounts to reduce shock and vibrational loads to the optical set-up during transport. A custom jacking system using electromechanical actuators was designed to affix the optical table directly to the ground through penetrations in the trailer floor. The jacking system allows remote sensing at longer ranges (up to 5 km) by eliminating jitter caused by wind or personnel movement within the trailer. A computer-controlled gimbal-mounted mirror was added to allow the laser beam to be accurately pointed in both the

  15. Practical Schemes for Accurate Forces in Quantum Monte Carlo.

    PubMed

    Moroni, S; Saccani, S; Filippi, C

    2014-11-11

    While the computation of interatomic forces has become a well-established practice within variational Monte Carlo (VMC), the use of the more accurate Fixed-Node Diffusion Monte Carlo (DMC) method is still largely limited to the computation of total energies on structures obtained at a lower level of theory. Algorithms to compute exact DMC forces have been proposed in the past, and one such scheme is also put forward in this work, but remain rather impractical due to their high computational cost. As a practical route to DMC forces, we therefore revisit here an approximate method, originally developed in the context of correlated sampling and named here the Variational Drift-Diffusion (VD) approach. We thoroughly investigate its accuracy by checking the consistency between the approximate VD force and the derivative of the DMC potential energy surface for the SiH and C2 molecules and employ a wide range of wave functions optimized in VMC to assess its robustness against the choice of trial function. We find that, for all but the poorest wave function, the discrepancy between force and energy is very small over all interatomic distances, affecting the equilibrium bond length obtained with the VD forces by less than 0.004 au. Furthermore, when the VMC forces are approximate due to the use of a partially optimized wave function, the DMC forces have smaller errors and always lead to an equilibrium distance in better agreement with the experimental value. We also show that the cost of computing the VD forces is only slightly larger than the cost of calculating the DMC energy. Therefore, the VD approximation represents a robust and efficient approach to compute accurate DMC forces, superior to the VMC counterparts.

  16. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  17. Fast and accurate predictions of covalent bonds in chemical space

    NASA Astrophysics Data System (ADS)

    Chang, K. Y. Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (˜1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H 2+ . Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  18. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  19. Chemical application of diffusion quantum Monte Carlo

    NASA Technical Reports Server (NTRS)

    Reynolds, P. J.; Lester, W. A., Jr.

    1984-01-01

    The diffusion quantum Monte Carlo (QMC) method gives a stochastic solution to the Schroedinger equation. This approach is receiving increasing attention in chemical applications as a result of its high accuracy. However, reducing statistical uncertainty remains a priority because chemical effects are often obtained as small differences of large numbers. As an example, the single-triplet splitting of the energy of the methylene molecule CH sub 2 is given. The QMC algorithm was implemented on the CYBER 205, first as a direct transcription of the algorithm running on the VAX 11/780, and second by explicitly writing vector code for all loops longer than a crossover length C. The speed of the codes relative to one another as a function of C, and relative to the VAX, are discussed. The computational time dependence obtained versus the number of basis functions is discussed and this is compared with that obtained from traditional quantum chemistry codes and that obtained from traditional computer architectures.

  20. Properties of Solar Thermal Fuels by Accurate Quantum Monte Carlo Calculations

    NASA Astrophysics Data System (ADS)

    Saritas, Kayahan; Ataca, Can; Grossman, Jeffrey C.

    2014-03-01

    Efficient utilization of the sun as a renewable and clean energy source is one of the major goals of this century due to increasing energy demand and environmental impact. Solar thermal fuels are materials that capture and store the sun's energy in the form of chemical bonds, which can then be released as heat on demand and charged again. Previous work on solar thermal fuels faced challenges related to the cyclability of the fuel over time, as well as the need for higher energy densities. Recently, it was shown that by templating photoswitches onto carbon nanostructures, both high energy density as well as high stability can be achieved. In this work, we explore alternative molecules to azobenzene in such a nano-templated system. We employ the highly accurate quantum Monte Carlo (QMC) method to predict the energy storage potential for each molecule. Our calculations show that in many cases the level of accuracy provided by density functional theory (DFT) is sufficient. However, in some cases, such as dihydroazulene, the drastic change in conjugation upon light absorption causes the DFT predictions to be inconsistent and incorrect. For this case, we compare our QMC results for the geometric structure, band gap and reaction enthalpy with different DFT functionals.

  1. Automated generation of quantum-accurate classical interatomic potentials for metals and semiconductors

    NASA Astrophysics Data System (ADS)

    Thompson, Aidan; Foiles, Stephen; Schultz, Peter; Swiler, Laura; Trott, Christian; Tucker, Garritt

    2013-03-01

    Molecular dynamics (MD) is a powerful condensed matter simulation tool for bridging between macroscopic continuum models and quantum models (QM) treating a few hundred atoms, but is limited by the accuracy of available interatomic potentials. Sound physical and chemical understanding of these interactions have resulted in a variety of concise potentials for certain systems, but it is difficult to extend them to new materials and properties. The growing availability of large QM data sets has made it possible to use more automated machine-learning approaches. Bartók et al. demonstrated that the bispectrum of the local neighbor density provides good regression surrogates for QM models. We adopt a similar bispectrum representation within a linear regression scheme. We have produced potentials for silicon and tantalum, and we are currently extending the method to III-V compounds. Results will be presented demonstrating the accuracy of these potentials relative to the training data, as well as their ability to accurately predict material properties not explicitly included in the training data. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Dept. of Energy Nat. Nuclear Security Admin. under Contract DE-AC04-94AL85000.

  2. Accurate Calculations of Rotationally Inelastic Scattering Cross Sections Using Mixed Quantum/Classical Theory.

    PubMed

    Semenov, Alexander; Babikov, Dmitri

    2014-01-16

    For computational treatment of rotationally inelastic scattering of molecules, we propose to use the mixed quantum/classical theory, MQCT. The old idea of treating translational motion classically, while quantum mechanics is used for rotational degrees of freedom, is developed to the new level and is applied to Na + N2 collisions in a broad range of energies. Comparison with full-quantum calculations shows that MQCT accurately reproduces all, even minor, features of energy dependence of cross sections, except scattering resonances at very low energies. The remarkable success of MQCT opens up wide opportunities for computational predictions of inelastic scattering cross sections at higher temperatures and/or for polyatomic molecules and heavier quenchers, which is computationally close to impossible within the full-quantum framework.

  3. Accurate Energy Spectrum for the Quantum Yang-Mills Mechanics with Nonlinear Color Oscillations

    NASA Astrophysics Data System (ADS)

    Pedram, Pouria

    2015-01-01

    Yang-Mills theory as the foundation for quantum chromodynamics is a non-Abelian gauge theory with self-interactions between vector particles. Here, we study the Yang-Mills Hamiltonian with nonlinear color oscillations in the absence of external sources corresponding to the group SU(2). In the quantum domain, we diagonalize the Hamiltonian using the optimized trigonometric basis expansion method and find accurate energy eigenvalues and eigenfunctions for one and two degrees of freedom. We also compare our results with the semiclassical solutions.

  4. Can accurate kinetic laws be created to describe chemical weathering?

    NASA Astrophysics Data System (ADS)

    Schott, Jacques; Oelkers, Eric H.; Bénézeth, Pascale; Goddéris, Yves; François, Louis

    2012-11-01

    Knowledge of the mechanisms and rates of mineral dissolution and growth, especially close to equilibrium, is essential for describing the temporal and spatial evolution of natural processes like weathering and its impact on CO2 budget and climate. The Surface Complexation approach (SC) combined with Transition State Theory (TST) provides an efficient framework for describing mineral dissolution over wide ranges of solution composition, chemical affinity, and temperature. There has been a large debate for several years, however, about the comparative merits of SC/TS versus classical growth theories for describing mineral dissolution and growth at near-to-equilibrium conditions. This study considers recent results obtained in our laboratory on oxides, hydroxides, silicates, and carbonates on near-equilibrium dissolution and growth via the combination of complementary microscopic and macroscopic techniques including hydrothermal atomic force microscopy, hydrogen-electrode concentration cell, mixed flow and batch reactors. Results show that the dissolution and precipitation of hydroxides, kaolinite, and hydromagnesite powders of relatively high BET surface area closely follow SC/TST rate laws with a linear dependence of both dissolution and growth rates on fluid saturation state (Ω) even at very close to equilibrium conditions (|ΔG| < 500 J/mol). This occurs because sufficient reactive sites (e.g. at kink, steps, and edges) are available at the exposed faces for dissolution and/or growth, allowing reactions to proceed via the direct and reversible detachment/attachment of reactants at the surface. In contrast, for magnesite and quartz, which have low surface areas, fewer active sites are available for growth and dissolution. Such minerals exhibit rates dependencies on Ω at near equilibrium conditions ranging from linear to highly non-linear functions of Ω, depending on the treatment of the crystals before the reaction. It follows that the form of the f

  5. Quantum dynamics of fast chemical reactions

    SciTech Connect

    Light, J.C.

    1993-12-01

    The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.

  6. Quantum chemical study of methane oxidation species

    NASA Technical Reports Server (NTRS)

    Jackels, Charles F.

    1993-01-01

    The research funded by this project has focused on quantum chemical investigations of molecular species thought to be important in the chemistry of the earth's upper and lower atmospheres. The body of this report contains brief discussions of the results of the several phases of this investigation. In many instances these results have been presented at scientific meetings and/or published in refereed journals. Those bibliographic references are given. In addition to the study of specific chemical systems, there were several phases during the course of this investigation where much of the effort went into the development and modification of computer codes necessary to carry out these calculations on the wide range of computer equipment used during this study. This type of code maintenance and development work did not generally result in publications and presentations, but a brief review is given.

  7. Quantum-Chemical Studies on TATB Processes

    NASA Astrophysics Data System (ADS)

    Patil, R. S.; Radhakrishnan, S.; Jadhav, P. M.; Ghule, V. D.; Soman, T.

    2010-04-01

    Quantum chemical studies have gained paramount importance in screening of thermodynamically feasible chemical processes. The current investigation attempts to select an appropriate process for the synthesis of 1,3,5-triamino-2,4,6-trinitro benzene (TATB), a reasonably powerful insensitive high explosive (IHE) through density functional theory (DFT) calculations. Although, 1,3,5-trichlorobenzene (TCB) and 1,3,5-trihydroxybenzene (THB) routes for synthesis of TATB have been well established, this article demonstrates the predictive capability of thermochemical computations for the identification of a viable process. Thermochemical parameters of reaction species have been obtained from DFT B3LYP/6-31G* calculations and feasibility of the process has been worked out on the basis of free energies of reactions and equilibrium constant as derived from standard enthalpy and entropy of the reaction species. The detailed computational studies have revealed that the THB route is thermodynamically feasible and the same has been supported experimentally.

  8. Chemical dynamics in the gas phase : quantum mechanics of chemical reactions.

    SciTech Connect

    Gray, S. K.

    2006-01-01

    This research program focuses on both the development and application of accurate quantum mechanical methods to describe gas phase chemical reactions and highly excited molecules. Emphasis is often placed on time-dependent or integrative approaches that, in addition to computational simplifications, yield useful mechanistic insights. Applications to systems of current experimental and theoretical interest are emphasized. The results of these calculations also allow one to gauge the quality of the underlying potential energy surfaces and the reliability of more approximate theoretical approaches such as classical trajectories and transition state theories.

  9. Ligand Affinities Estimated by Quantum Chemical Calculations.

    PubMed

    Söderhjelm, Pär; Kongsted, Jacob; Ryde, Ulf

    2010-05-11

    We present quantum chemical estimates of ligand-binding affinities performed, for the first time, at a level of theory for which there is a hope that dispersion and polarization effects are properly accounted for (MP2/cc-pVTZ) and at the same time effects of solvation, entropy, and sampling are included. We have studied the binding of seven biotin analogues to the avidin tetramer. The calculations have been performed by the recently developed PMISP approach (polarizable multipole interactions with supermolecular pairs), which treats electrostatic interactions by multipoles up to quadrupoles, induction by anisotropic polarizabilities, and nonclassical interactions (dispersion, exchange repulsion, etc.) by explicit quantum chemical calculations, using a fragmentation approach, except for long-range interactions that are treated by standard molecular-mechanics Lennard-Jones terms. In order to include effects of sampling, 10 snapshots from a molecular dynamics simulation are studied for each biotin analogue. Solvation energies are estimated by the polarized continuum model (PCM), coupled to the multipole-polarizability model. Entropy effects are estimated from vibrational frequencies, calculated at the molecular mechanics level. We encounter several problems, not previously discussed, illustrating that we are first to apply such a method. For example, the PCM model is, in the present implementation, questionable for large molecules, owing to the use of a surface definition that gives numerous small cavities in a protein. PMID:26615702

  10. [Significance of quantum chemical interactions for medicinal science and design of β-secretase inhibitors].

    PubMed

    Hamada, Yoshio

    2013-01-01

    This review discusses the importance of quantum chemical interactions in biomolecules for medicinal science and their relevance to the author's β-secretase (BACE1) inhibitor drug discovery research. Although molecular mechanics/dynamics (MM/MD) methods are available in many in silico design tools used for drug discovery, they cannot accurately evaluate quantum effects between biomolecules and drugs. The key roles of biomolecular quantum chemical interactions in drug discovery are discussed using the arginine side chain as an example. Arginine is recognized as a charged amino acid in commonly used drug design software, unlike other amino acids with π-electron orbitals, such as phenylalanine, tyrosine, and tryptophan. Quantum chemical interactions via the arginine side chain are crucial for molecular recognition, and are found in many X-ray crystal structures, such as protein-protein, protein homodimer, RNA aptamer-protein, and enzyme-inhibitor complexes. This review describes the essential role of quantum chemical interactions via the arginine side chain in the mechanism of BACE1 inhibition, and proposes an "electron donor/acceptor bioisostere" concept for medicinal science based on quantum chemical interactions. Several potent BACE1 inhibitors, as well as the first peptides with BACE1 inhibiting activity were designed and synthesized based on studies of quantum chemical interactions via arginine side chain and the "electron donor bioisostere" concept.

  11. Quantum chemical variables in QSAR: A review

    SciTech Connect

    Hickey, J.P.; Passino-Reader, D.R.

    1994-12-31

    The integration of molecular orbital calculations with QSAR analyses has resulted in many ``theoretical`` indices. The authors will present a brief overview of these numerous quantum chemical parameters used in QSAR, as well as a small sampling of their applications (e.g., correlation of carcinogenicity with structure for PAHS, and MO calculations to predict toxicity of PCDDs and PCDFS). The quantum mechanical indices described here are compiled from many sources and are generally obtained from classical molecular mechanical methods, as well as from calculated molecular wavefunctions. The quality of the model or wave function and, consequently, of the indices depend entirely on the formalism and the level of approximation used. Because the molecular waveform is often described as a linear combination of atomic orbitals (LCAO), one can easily obtain some of the indices. These include the atomic charges, sigma and pi charges, frontier electron densities, E{sub HOMO}, and E{sub LUMA} and the superdelocalizability parameters. Parameter computation methods and appropriate software (and sources) will be highlighted.

  12. Simple and accurate quantification of quantum dots via single-particle counting.

    PubMed

    Zhang, Chun-yang; Johnson, Lawrence W

    2008-03-26

    Quantification of quantum dots (QDs) is essential to the quality control of QD synthesis, development of QD-based LEDs and lasers, functionalizing of QDs with biomolecules, and engineering of QDs for biological applications. However, simple and accurate quantification of QD concentration in a variety of buffer solutions and in complex mixtures still remains a critical technological challenge. Here, we introduce a new methodology for quantification of QDs via single-particle counting, which is conceptually different from established UV-vis absorption and fluorescence spectrum techniques where large amounts of purified QDs are needed and specific absorption coefficient or quantum yield values are necessary for measurements. We demonstrate that single-particle counting allows us to nondiscriminately quantify different kinds of QDs by their distinct fluorescence burst counts in a variety of buffer solutions regardless of their composition, structure, and surface modifications, and without the necessity of absorption coefficient and quantum yield values. This single-particle counting can also unambiguously quantify individual QDs in a complex mixture, which is practically impossible for both UV-vis absorption and fluorescence spectrum measurements. Importantly, the application of this single-particle counting is not just limited to QDs but also can be extended to fluorescent microspheres, quantum dot-based microbeads, and fluorescent nano rods, some of which currently lack efficient quantification methods.

  13. An accurate single-electron pump based on a highly tunable silicon quantum dot.

    PubMed

    Rossi, Alessandro; Tanttu, Tuomo; Tan, Kuan Yen; Iisakka, Ilkka; Zhao, Ruichen; Chan, Kok Wai; Tettamanzi, Giuseppe C; Rogge, Sven; Dzurak, Andrew S; Möttönen, Mikko

    2014-06-11

    Nanoscale single-electron pumps can be used to generate accurate currents, and can potentially serve to realize a new standard of electrical current based on elementary charge. Here, we use a silicon-based quantum dot with tunable tunnel barriers as an accurate source of quantized current. The charge transfer accuracy of our pump can be dramatically enhanced by controlling the electrostatic confinement of the dot using purposely engineered gate electrodes. Improvements in the operational robustness, as well as suppression of nonadiabatic transitions that reduce pumping accuracy, are achieved via small adjustments of the gate voltages. We can produce an output current in excess of 80 pA with experimentally determined relative uncertainty below 50 parts per million.

  14. Thermochemistry and Charge Delocalization in Cyclization Reactions Using Accurate Quantum Monte Carlo Calculations

    NASA Astrophysics Data System (ADS)

    Saritas, Kayahan; Grossman, Jeffrey C.

    2015-03-01

    Molecules that undergo pericyclic isomerization reactions find interesting optical and energy storage applications, because of their usually high quantum yields, large spectral shifts and small structural changes upon light absorption. These reactions induce a drastic change in the conjugated structure such that substituents that become a part of the conjugated system upon isomerization can play an important role in determining properties such as enthalpy of isomerization and HOMO-LUMO gap. Therefore, theoretical investigations dealing with such systems should be capable of accurately capturing the interplay between electron correlation and exchange effects. In this work, we examine the dihydroazulene isomerization as an example conjugated system. We employ the highly accurate quantum Monte Carlo (QMC) method to predict thermochemical properties and to benchmark results from density functional theory (DFT) methods. Although DFT provides sufficient accuracy for similar systems, in this particular system, DFT predictions of ground state and reaction paths are inconsistent and non-systematic errors arise. We present a comparison between QMC and DFT results for enthalpy of isomerization, HOMO-LUMO gap and charge densities with a range of DFT functionals.

  15. Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry.

    PubMed

    Ryde, Ulf

    2007-02-14

    The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.

  16. Remote chemical sensing with quantum cascade lasers

    SciTech Connect

    Harper, Warren W.; Strasburg, Jana D.

    2004-10-15

    A trailer based sensor system has been developed for remote chemical sensing applications. The sensor uses quantum cascade lasers (QCL) that operate in the long wave infrared. The QCL is operated continuous wave, and its wavelength is both ramped over a molecular absorption feature and frequency modulated. Lock-in techniques are used to recover weak laser return signals. Field experiments have monitored ambient water vapor and small quantities of nitrous oxide, tetrafluoroethane (R134a), and hydrogen sulfide released as atmospheric plumes. Round trip path lengths up to 10 km were obtained using a retro-reflector. Atmospheric turbulence was found to be the dominating noise source. It causes intensity fluctuations in the received power, which can significantly degrade the sensor performance. Unique properties associated with QCLs enabled single beam normalization techniques to be implemented thus reducing the impact that turbulence has on experimental signal to noise. Weighted data averaging was additionally used to increase the signal to noise of data traces. Absorbance sensitivities as low as {approx}1 x 10{sup -4} could be achieved with 5 seconds of data averaging, even under high turbulence conditions.

  17. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.

    PubMed

    Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L

    2016-01-01

    Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples.

  18. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.

    PubMed

    Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L

    2016-01-01

    Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples. PMID:27498635

  19. A time-accurate implicit method for chemical non-equilibrium flows at all speeds

    NASA Technical Reports Server (NTRS)

    Shuen, Jian-Shun

    1992-01-01

    A new time accurate coupled solution procedure for solving the chemical non-equilibrium Navier-Stokes equations over a wide range of Mach numbers is described. The scheme is shown to be very efficient and robust for flows with velocities ranging from M less than or equal to 10(exp -10) to supersonic speeds.

  20. pK(a) prediction from "Quantum Chemical Topology" descriptors.

    PubMed

    Harding, A P; Wedge, D C; Popelier, P L A

    2009-08-01

    Knowing the pK(a) of a compound gives insight into many properties relevant to many industries, in particular the pharmaceutical industry during drug development processes. In light of this, we have used the theory of Quantum Chemical Topology (QCT), to provide ab initio descriptors that are able to accurately predict pK(a) values for 228 carboxylic acids. This Quantum Topological Molecular Similarity (QTMS) study involved the comparison of 5 increasingly more expensive levels of theory to conclude that HF/6-31G(d) and B3LYP/6-311+G(2d,p) provided an accurate representation of the compounds studies. We created global and subset models for the carboxylic acids using Partial Least Square (PLS), Support Vector Machines (SVM), and Radial Basis Function Neural Networks (RBFNN). The models were extensively validated using 4-, 7-, and 10-fold cross-validation, with the validation sets selected based on systematic and random sampling. HF/6-31G(d) in conjunction with SVM provided the best statistics when taking into account the large increase in CPU time required to optimize the geometries at the B3LYP/6-311+G(2d,p) level. The SVM models provided an average q(2) value of 0.886 and an RMSE value of 0.293 for all the carboxylic acids, a q(2) of 0.825 and RMSE of 0.378 for the ortho-substituted acids, a q(2) of 0.923 and RMSE of 0.112 for the para- and meta-substituted acids, and a q(2) of 0.906 and RMSE of 0.268 for the aliphatic acids. Our method compares favorably to ACD/Laboratories, VCCLAB, SPARC, and ChemAxon's pK(a) prediction software based of the RMSE calculated by the leave-one-out method.

  1. Quantum chemical interaction energy surfaces of ethylene and propene dimers.

    PubMed

    Jalkanen, Jukka-Pekka; Pulkkinen, Sallaraisa; Pakkanen, Tapani A; Rowley, Richard L

    2005-03-31

    Ab initio studies of nonbonding interactions for ethylene and propene dimers were conducted at the MP2/6-311+G(2df,2pd) level. The dimers were attractive in all of the orientations studied; however, the attraction was <0.1 kcal/mol for ethylene D2h and C2h dimers, for which the pi-electron clouds or H atoms interact closely. A previously introduced transferable potential model, NIPE [Jalkanen, J.-P.; Pakkanen, T. A.; Yang, Y.; Rowley, R. L. J. Chem. Phys. 2003, 118, 5474], which is based on quantum chemical calculations of small alkane molecules, was tested against the propene and ethylene dimer data. Comparisons of results showed that interaction energies for orientations dominated by interactions between the propene methyl groups or two hydrogens were accurately predicted with the NIPE model. Interactions involving the double bond were not predicted as well, because the original NIPE regression data set did not contain any information about pi-electron systems. An extension of the NIPE model to include pi-electron interactions is proposed. Additional interaction sites are used with the same energy function as atomic interactions. This addition provides a more accurate description of the interaction energies of both ethylene and propene and extends the transferability of the NIPE model to alkenes.

  2. Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes

    DOE PAGES

    Sjostrom, Travis; Daligault, Jerome

    2014-10-10

    Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lowermore » temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.« less

  3. Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes

    SciTech Connect

    Sjostrom, Travis; Daligault, Jerome

    2014-10-10

    Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lower temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.

  4. Accurate non-adiabatic quantum dynamics from pseudospectral sampling of time-dependent Gaussian basis sets

    NASA Astrophysics Data System (ADS)

    Heaps, Charles W.; Mazziotti, David A.

    2016-08-01

    Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schrödinger equation with N Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from O ( N 2 ) to O ( N ) . By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing the nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems: the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-dimensional model for collinear triatomic vibrational dynamics. In all cases, the pseudospectral Gaussian method is in quantitative agreement with numerically exact calculations. The results are promising for nonadiabatic molecular dynamics in molecular systems where strongly correlated ground or excited states require expensive electronic structure calculations.

  5. Remote Chemical Sensing Using Quantum Cascade Lasers

    SciTech Connect

    Harper, Warren W.; Strasburg, Jana D.; Aker, Pam M.; Schultz, John F.

    2004-01-20

    instrument detection limit. The range of chemicals detectable by FM DIAL has also been extended. Prior to FY03 only water and nitrous oxide (N2O) had been seen. Experiments on extending the tuning range of the quantum cascade laser (QCL) currently used in the experiments demonstrate that many more species are now accessible including H2S, C2F4H2, and CH4. We additionally demonstrated that FM DIAL measurements can be made using short wave infrared (SWIR) telecommunications lasers. While measurements made using these components are noisier because turbulence and particulate matter cause more interference in this spectral region, monitoring in this region enables larger species to be detected simply because these lasers have a greater tuning range. In addition, SWIR monitoring also allows for the detection of second-row hydride species such as HF and HCl, which are important nuclear and CWA proliferation signatures.

  6. Stereodynamics of chemical reactions: quasi-classical, quantum and mixed quantum-classical theories

    NASA Astrophysics Data System (ADS)

    Xu, Wenwu; Zhao, Guangjiu

    2012-04-01

    In this review, some benchmark works by Han and coworkers on the stereodynamics of typical chemical reactions, triatomic reactions H + D2, Cl + H2 and O + H2 and polyatomic reaction Cl+CH4/CD4, are presented by using the quasi-classical, quantum and mixed quantum-classical methods. The product alignment and orientation in these A+BC model reactions are discussed in detail. We have also compared our theoretical results with experimental measurements and demonstrated that our theoretical results are in good agreement with the experimental results. Quasi-classical trajectory (QCT) method ignores some quantum effects like the tunneling effect and zero-point energy. The quantum method will be very time-consuming. Moreover, the mixed quantum-classical method can take into account some quantum effects and hence is expected to be applicable to large systems and widely used in chemical stereodynamics studies.

  7. Chemically accurate energy barriers of small gas molecules moving through hexagonal water rings.

    PubMed

    Hjertenæs, Eirik; Trinh, Thuat T; Koch, Henrik

    2016-07-21

    We present chemically accurate potential energy curves of CH4, CO2 and H2 moving through hexagonal water rings, calculated by CCSD(T)/aug-cc-pVTZ with counterpoise correction. The barriers are extracted from a potential energy surface obtained by allowing the water ring to expand while the gas molecule diffuses through. State-of-the-art XC-functionals are evaluated against the CCSD(T) potential energy surface.

  8. An accurate quantum expression of the z-dipole matrix element between nearby Rydberg parabolic states and the correspondence principle

    NASA Astrophysics Data System (ADS)

    Dewangan, D. P.

    2008-01-01

    We give an exact quantum formula for the z-component of the dipole matrix element between parabolic states of a hydrogen atom in terms of the Jacobi polynomials. The formula extends the range of numerical computation to larger values of the parabolic quantum numbers for which computation from the standard textbook formula, which is in terms of the hypergeometric functions, is defined. We obtain an accurate quantum expression of the z-dipole matrix element in terms of the ordinary Bessel functions for transition between nearby Rydberg parabolic states. We derive for the first time the formula of the z-dipole matrix element of the correspondence principle method directly from the quantum expression, and in the process of derivation, clarify the nature of classical-quantum correspondence. The expressions obtained in this work solve the problem of computation of the z-dipole matrix element of hydrogen to a large extent.

  9. Computational Chemical Imaging for Cardiovascular Pathology: Chemical Microscopic Imaging Accurately Determines Cardiac Transplant Rejection

    PubMed Central

    Tiwari, Saumya; Reddy, Vijaya B.; Bhargava, Rohit; Raman, Jaishankar

    2015-01-01

    Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR) spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients’ biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures. PMID:25932912

  10. A quantum accurate waveform synthesizer as a voltage reference for an electronic primary thermometer

    NASA Astrophysics Data System (ADS)

    Pollarolo, Alessio; Benz, Samuel; Rogalla, Horst; Dresselhaus, Paul

    2014-03-01

    We are using a quantum voltage noise source (QVNS) for use as an intrinsically accurate voltage reference for a new type of electronic temperature standard. In Johnson Noise Thermometry (JNT) the noise of a resistor is used to measure temperature or Boltzmann's constant k, because the Nyquist equation =4kTR Δf shows that the power spectral density is proportional to k, temperature T, resistance R and measurement bandwidth Δf . The QVNS is a digital to analog converter used to synthesize a voltage waveform that resembles pseudo-random noise comparable in amplitude to the resistor noise. The signal generated is a frequency comb of harmonics tones that are equally spaced in frequency, all having identical amplitudes but random phases. The QVNS is an array superconducting Josephson junctions that are biased with a pulsed waveform clocked at 10 GHz. The accuracy of the voltage waveform derives from the identical voltage pulses produced by each junction that are perfectly quantized because their time-integrals are always equal to flux quantum h/2 e. The time-dependent output voltage waveform is determined by the number of pulses and their density in time. The measurement electronics exploits cross-correlation techniques to reduce the uncorrelated measurement noise so as to reveal the resistor noise, both of which are on the order of 2 nV/ √Hz. With this technique we have measured k with an uncertainty of about one part in 105, which we hope to improve by another order of magnitude with further research.

  11. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

    PubMed

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O Anatole; Müller, Klaus-Robert; Tkatchenko, Alexandre

    2015-06-18

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  12. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    SciTech Connect

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  13. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  14. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    PubMed Central

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  15. Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.

    PubMed

    Zhu, Tong; Zhang, John Z H; He, Xiao

    2015-01-01

    The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the Poisson-Boltzmann (PB) model and first solvation water molecules, the influence of solvent effect is also discussed. Benefiting from the fragmentation algorithm, the AF-QM/MM approach is computationally efficient, linear-scaling with a low pre-factor, and thus can be applied to routinely calculate the ab initio NMR chemical shifts for proteins of any size. The results calculated using Density Functional Theory (DFT) show that when the solvent effect is included, this method can accurately reproduce the experimental ¹H NMR chemical shifts, while the ¹³C NMR chemical shifts are less affected by the solvent. However, although the inclusion of solvent effect shows significant improvement for ¹⁵N chemical shifts, the calculated values still have large deviations from the experimental observations. Our study further demonstrates that AF-QM/MM calculated results accurately reflect the dependence of ¹³C(α) NMR chemical shifts on the secondary structure of proteins, and the calculated ¹H chemical shift can be utilized to discriminate the native structure of proteins from decoys.

  16. Multiple-Resonance Local Wave Functions for Accurate Excited States in Quantum Monte Carlo.

    PubMed

    Zulfikri, Habiburrahman; Amovilli, Claudio; Filippi, Claudia

    2016-03-01

    We introduce a novel class of local multideterminant Jastrow-Slater wave functions for the efficient and accurate treatment of excited states in quantum Monte Carlo. The wave function is expanded as a linear combination of excitations built from multiple sets of localized orbitals that correspond to the bonding patterns of the different Lewis resonance structures of the molecule. We capitalize on the concept of orbital domains of local coupled-cluster methods, which is here applied to the active space to select the orbitals to correlate and construct the important transitions. The excitations are further grouped into classes, which are ordered in importance and can be systematically included in the Jastrow-Slater wave function to ensure a balanced description of all states of interest. We assess the performance of the proposed wave function in the calculation of vertical excitation energies and excited-state geometry optimization of retinal models whose π → π* state has a strong intramolecular charge-transfer character. We find that our multiresonance wave functions recover the reference values of the total energies of the ground and excited states with only a small number of excitations and that the same expansion can be flexibly used at very different geometries. Furthermore, significant computational saving can also be gained in the orbital optimization step by selectively mixing occupied and virtual orbitals based on spatial considerations without loss of accuracy on the excitation energy. Our multiresonance wave functions are therefore compact, accurate, and very promising for the calculation of multiple excited states of different character in large molecules.

  17. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    SciTech Connect

    Thompson, A.P.; Swiler, L.P.; Trott, C.R.; Foiles, S.M.; Tucker, G.J.

    2015-03-15

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

  18. Accurate band gaps of semiconductors and insulators from Quantum Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Nazarov, Roman; Hood, Randolph; Morales, Miguel

    2015-03-01

    Ab initio calculations are useful tools in developing materials with targeted band gaps for semiconductor industry. Unfortunately, the main workhorse of ab initio calculations - density functional theory (DFT) in local density approximation (LDA) or generalized gradient approximation (GGA) underestimates band gaps. Several approaches have been proposed starting from empirical corrections to more elaborate exchange-correlation functionals to deal with this problem. But none of these work well for the entire range of semiconductors and insulators. Deficiencies of DFT as a mean field method can be overcome using many-body techniques. Quantum Monte Carlo (QMC) methods can obtain a nearly exact numerical solutions of both total energies and spectral properties. Diffusion Monte Carlo (DMC), the most widely used QMC method, has been shown to provide gold standard results for different material properties, including spectroscopic constants of dimers and clusters, equation of state for solids, accurate descriptions of defects in metals and insulators. To test DMC's accuracy in a wider range of semiconductors and insulators we have computed band gaps of several semiconductors and insulators. We show that DMC can provide superior agreement with experiment compared with more traditional DFT approaches including high level exchange-correlation functionals (e.g. HSE).

  19. Accurate reliability analysis method for quantum-dot cellular automata circuits

    NASA Astrophysics Data System (ADS)

    Cui, Huanqing; Cai, Li; Wang, Sen; Liu, Xiaoqiang; Yang, Xiaokuo

    2015-10-01

    Probabilistic transfer matrix (PTM) is a widely used model in the reliability research of circuits. However, PTM model cannot reflect the impact of input signals on reliability, so it does not completely conform to the mechanism of the novel field-coupled nanoelectronic device which is called quantum-dot cellular automata (QCA). It is difficult to get accurate results when PTM model is used to analyze the reliability of QCA circuits. To solve this problem, we present the fault tree models of QCA fundamental devices according to different input signals. After that, the binary decision diagram (BDD) is used to quantitatively investigate the reliability of two QCA XOR gates depending on the presented models. By employing the fault tree models, the impact of input signals on reliability can be identified clearly and the crucial components of a circuit can be found out precisely based on the importance values (IVs) of components. So this method is contributive to the construction of reliable QCA circuits.

  20. Neural network approach to quantum-chemistry data: Accurate prediction of density functional theory energies

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.; Lomakina, Ekaterina I.

    2009-08-01

    Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.

  1. Forming NCO(-) in Dense Molecular Clouds: Possible Gas-Phase Chemical Paths From Quantum Calculations.

    PubMed

    Yurtsever, E; Gianturco, F A; Wester, R

    2016-07-14

    The existence of NCO(-) anions in the interstellar medium (ISM) has been suggested and searched for over the years but without any formal definitive sighting of that molecule. We discuss in this work the possible formation of either NCO(-) directly or of NCO neutral as a precursor to NCO(-) formation by electron attachment. We follow simple, gas-phase chemical reactions for which the general features are obtained from accurate quantum calculations. The results are shedding some additional light on the likely presence of this anion in the ISM environment, drawing further information from the specific features of the considered reactions on the additional chemical options that exist for its formation.

  2. Halogen bonded supramolecular capsules: a challenging test case for quantum chemical methods.

    PubMed

    Sure, Rebecca; Grimme, Stefan

    2016-08-01

    Recently, Diederich et al. synthesized the first supramolecular capsule with a well-defined four-point halogen bonding interaction [Angew. Chem., Int. Ed., 2015, 54, 12339]. This interesting system comprising about 400 atoms represents a challenging test case for accurate quantum chemical methods. We investigate it with our new density functional based composite method for structures and noncovalent interactions (PBEh-3c) as well as our standard protocol for supramolecular thermochemistry and give predictions for chemical modifications to improve the binding strength. PMID:27416814

  3. Forming NCO– in Dense Molecular Clouds: Possible Gas-Phase Chemical Paths From Quantum Calculations

    PubMed Central

    2015-01-01

    The existence of NCO– anions in the interstellar medium (ISM) has been suggested and searched for over the years but without any formal definitive sighting of that molecule. We discuss in this work the possible formation of either NCO– directly or of NCO neutral as a precursor to NCO– formation by electron attachment. We follow simple, gas-phase chemical reactions for which the general features are obtained from accurate quantum calculations. The results are shedding some additional light on the likely presence of this anion in the ISM environment, drawing further information from the specific features of the considered reactions on the additional chemical options that exist for its formation. PMID:26696323

  4. Accurate dispensing of volatile reagents on demand for chemical reactions in EWOD chips

    PubMed Central

    Ding, Huijiang; Sadeghi, Saman; Shah, Gaurav J.; Chen, Supin; Keng, Pei Yuin; Kim, Chang-Jin “CJ”; van Dam, R. Michael

    2015-01-01

    Digital microfluidic chips provide a new platform for manipulating chemicals for multi-step chemical synthesis or assays at the microscale. The organic solvents and reagents needed for these applications are often volatile, sensitive to contamination, and wetting, i.e. have contact angles of < 90° even on the highly hydrophobic surfaces (e.g., Teflon® or Cytop®) typically used on digital microfluidic chips. Furthermore, often the applications dictate that the processes are performed in a gas environment, not allowing the use of a filler liquid (e.g., oil). These properties pose challenges for delivering controlled volumes of liquid to the chip. An automated, simple, accurate and reliable method of delivering reagents from sealed, off-chip reservoirs is presented here. This platform overcomes the issues of evaporative losses of volatile solvents, cross-contamination, and flooding of the chip by combining a syringe pump, a simple on-chip liquid detector and a robust interface design. The impedance-based liquid detection requires only minimal added hardware to provide a feedback signal to ensure accurate volumes of volatile solvents are introduced to the chip, independent of time delays between dispensing operations. On-demand dispensing of multiple droplets of acetonitrile, a frequently used but difficult to handle solvent due to its wetting properties and volatility, was demonstrated and used to synthesize the positron emission tomography (PET) probe [18F]FDG reliably. PMID:22825699

  5. Accurate dispensing of volatile reagents on demand for chemical reactions in EWOD chips.

    PubMed

    Ding, Huijiang; Sadeghi, Saman; Shah, Gaurav J; Chen, Supin; Keng, Pei Yuin; Kim, Chang-Jin C J; van Dam, R Michael

    2012-09-21

    Digital microfluidic chips provide a new platform for manipulating chemicals for multi-step chemical synthesis or assays at the microscale. The organic solvents and reagents needed for these applications are often volatile, sensitive to contamination, and wetting, i.e. have contact angles of <90° even on the highly hydrophobic surfaces (e.g., Teflon® or Cytop®) typically used on digital microfluidic chips. Furthermore, often the applications dictate that the processes are performed in a gas environment, not allowing the use of a filler liquid (e.g., oil). These properties pose challenges for delivering controlled volumes of liquid to the chip. An automated, simple, accurate and reliable method of delivering reagents from sealed, off-chip reservoirs is presented here. This platform overcomes the issues of evaporative losses of volatile solvents, cross-contamination, and flooding of the chip by combining a syringe pump, a simple on-chip liquid detector and a robust interface design. The impedance-based liquid detection requires only minimal added hardware to provide a feedback signal to ensure accurate volumes of volatile solvents are introduced to the chip, independent of time delays between dispensing operations. On-demand dispensing of multiple droplets of acetonitrile, a frequently used but difficult to handle solvent due to its wetting properties and volatility, was demonstrated and used to synthesize the positron emission tomography (PET) probe [(18)F]FDG reliably.

  6. Limits and potentials of quantum chemical methods in modelling photosynthetic antennae.

    PubMed

    Jurinovich, Sandro; Viani, Lucas; Curutchet, Carles; Mennucci, Benedetta

    2015-12-14

    Advances in electronic spectroscopies with femtosecond time resolution have provided new information on the excitonic processes taking place during the energy conversion in natural photosynthetic antennae. This has promoted the development of new theoretical protocols aiming at accurately describing the properties and mechanisms of exciton formation and relaxation. In this perspective, we provide an overview of the quantum chemical based approaches, trying to underline both the potentials of the methods and their weaknesses. In particular three main aspects will be analysed, the quantum mechanical description of excitonic parameters (site energies and couplings), the incorporation of environmental effects on these parameters through hybrid quantum/classical approaches, and the modelling of the dynamical coupling among such parameters and the vibrations of the pigment-protein complex. PMID:25865958

  7. Remote Chemical Sensing Using Quantum Cascade Lasers

    SciTech Connect

    Harper, Warren W.; Schultz, John F.

    2003-01-30

    Spectroscopic chemical sensing research at Pacific Northwest National Laboratory (PNNL) is focused on developing advanced sensors for detecting the production of nuclear, chemical, or biological weapons; use of chemical weapons; or the presence of explosives, firearms, narcotics, or other contraband of significance to homeland security in airports, cargo terminals, public buildings, or other sensitive locations. For most of these missions, the signature chemicals are expected to occur in very low concentrations, and in mixture with ambient air or airborne waste streams that contain large numbers of other species that may interfere with spectroscopic detection, or be mistaken for signatures of illicit activity. PNNL’s emphasis is therefore on developing remote and sampling sensors with extreme sensitivity, and resistance to interferents, or selectivity. PNNL’s research activities include: 1. Identification of signature chemicals and quantification of their spectral characteristics, 2. Identification and development of laser and other technologies that enable breakthroughs in sensitivity and selectivity, 3. Development of promising sensing techniques through experimentation and modeling the physical phenomenology and practical engineering limitations affecting their performance, and 4. Development and testing of data collection methods and analysis algorithms. Close coordination of all aspects of the research is important to ensure that all parts are focused on productive avenues of investigation. Close coordination of experimental development and numerical modeling is particularly important because the theoretical component provides understanding and predictive capability, while the experiments validate calculations and ensure that all phenomena and engineering limitations are considered.

  8. Quantum chemical parameters in QSAR: what do I use when?

    USGS Publications Warehouse

    Hickey, James P.; Ostrander, Gary K.

    1996-01-01

    This chapter provides a brief overview of the numerous quantum chemical parameters that have been/are currently being used in quantitative structure activity relationships (QSAR), along with a representative bibliography. The parameters will be grouped according to their mechanistic interpretations, and representative biological and physical chemical applications will be mentioned. Parmater computation methods and the appropriate software are highlighted, as are sources for software.

  9. Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

    PubMed

    Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

    2014-11-12

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

  10. Quantum and semiclassical theories of chemical reaction rates

    SciTech Connect

    Miller, W.H. |

    1995-09-01

    A rigorous quantum mechanical theory (and a semiclassical approximation thereto) is described for calculating chemical reaction rates ``directly``, i.e., without having to solve the complete state-to-state reactive scattering problem. The approach has many vestiges of transition state theory, for which it may be thought of as the rigorous generalization.

  11. Dynamical mean-field theory from a quantum chemical perspective.

    PubMed

    Zgid, Dominika; Chan, Garnet Kin-Lic

    2011-03-01

    We investigate the dynamical mean-field theory (DMFT) from a quantum chemical perspective. Dynamical mean-field theory offers a formalism to extend quantum chemical methods for finite systems to infinite periodic problems within a local correlation approximation. In addition, quantum chemical techniques can be used to construct new ab initio Hamiltonians and impurity solvers for DMFT. Here, we explore some ways in which these things may be achieved. First, we present an informal overview of dynamical mean-field theory to connect to quantum chemical language. Next, we describe an implementation of dynamical mean-field theory where we start from an ab initio Hartree-Fock Hamiltonian that avoids double counting issues present in many applications of DMFT. We then explore the use of the configuration interaction hierarchy in DMFT as an approximate solver for the impurity problem. We also investigate some numerical issues of convergence within DMFT. Our studies are carried out in the context of the cubic hydrogen model, a simple but challenging test for correlation methods. Finally, we finish with some conclusions for future directions.

  12. Accurate nonadiabatic quantum dynamics on the cheap: Making the most of mean field theory with master equations

    SciTech Connect

    Kelly, Aaron; Markland, Thomas E.; Brackbill, Nora

    2015-03-07

    In this article, we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.

  13. Accurate nonadiabatic quantum dynamics on the cheap: making the most of mean field theory with master equations.

    PubMed

    Kelly, Aaron; Brackbill, Nora; Markland, Thomas E

    2015-03-01

    In this article, we show how Ehrenfest mean field theory can be made both a more accurate and efficient method to treat nonadiabatic quantum dynamics by combining it with the generalized quantum master equation framework. The resulting mean field generalized quantum master equation (MF-GQME) approach is a non-perturbative and non-Markovian theory to treat open quantum systems without any restrictions on the form of the Hamiltonian that it can be applied to. By studying relaxation dynamics in a wide range of dynamical regimes, typical of charge and energy transfer, we show that MF-GQME provides a much higher accuracy than a direct application of mean field theory. In addition, these increases in accuracy are accompanied by computational speed-ups of between one and two orders of magnitude that become larger as the system becomes more nonadiabatic. This combination of quantum-classical theory and master equation techniques thus makes it possible to obtain the accuracy of much more computationally expensive approaches at a cost lower than even mean field dynamics, providing the ability to treat the quantum dynamics of atomistic condensed phase systems for long times.

  14. Investigation of quantum confinement behavior of zinc sulphide quantum dots synthesized via various chemical methods

    SciTech Connect

    Jose, Meera Sakthivel, T. Chandran, Hrisheekesh T. Nivea, R. Gunasekaran, V.

    2014-10-15

    In this work, undoped and Ag-doped ZnS quantum dots were synthesized using various chemical methods. The products were characterized using X-ray diffraction (XRD), UV-visible spectroscopy and Photoluminescence spectroscopy. Our results revealed that the size of the as-prepared samples range from 1–6 nm in diameter and have a cubic zinc-blende structure. Also, we observed the emission of different wavelength of light from different sized quantum dots of the same material due to quantum confinement effect. The results will be presented in detail and ZnS can be a potential candidate for optical device development and applications.

  15. Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

    NASA Astrophysics Data System (ADS)

    Hu, Hao; Yang, Weitao

    2008-05-01

    Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.

  16. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

    PubMed

    Hu, Hao; Yang, Weitao

    2008-01-01

    Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.

  17. Accurate heteronuclear J-coupling measurements in dilute spin systems using the multiple-quantum filtered J-resolved experiment.

    PubMed

    Martineau, Charlotte; Fayon, Franck; Legein, Christophe; Buzaré, Jean-Yves; Silly, Gilles; Massiot, Dominique

    2007-07-14

    A new solid-state MAS NMR experiment is proposed to accurately measure heteronuclear (19)F-(207)Pb J-coupling constants, even though these couplings are not visible on high speed (19)F 1D MAS spectra; in particular, we demonstrate that the J-resolved experiment combined with scalar multiple-quantum filtering considerably improves the resolution of J-multiplet patterns for dilute spin systems. PMID:17594032

  18. A time-accurate implicit method for chemically reacting flows at all Mach numbers

    NASA Technical Reports Server (NTRS)

    Withington, J. P.; Yang, V.; Shuen, J. S.

    1991-01-01

    The objective of this work is to develop a unified solution algorithm capable of treating time-accurate chemically reacting flows at all Mach numbers, ranging from molecular diffusion velocities to supersonic speeds. A rescaled pressure term is used in the momentum equation to circumvent the singular behavior of pressure at low Mach numbers. A dual time-stepping integration procedure is established. The system eigenvalues become well behaved and have the same order of magnitude, even in the very low Mach number regime. The computational efficiency for moderate and high speed flow is competitive with the conventional density-based scheme. The capabilities of the algorithm are demonstrated by applying it to selected model problems including nozzle flows and flame dynamics.

  19. A time-accurate algorithm for chemical non-equilibrium viscous flows at all speeds

    NASA Technical Reports Server (NTRS)

    Shuen, J.-S.; Chen, K.-H.; Choi, Y.

    1992-01-01

    A time-accurate, coupled solution procedure is described for the chemical nonequilibrium Navier-Stokes equations over a wide range of Mach numbers. This method employs the strong conservation form of the governing equations, but uses primitive variables as unknowns. Real gas properties and equilibrium chemistry are considered. Numerical tests include steady convergent-divergent nozzle flows with air dissociation/recombination chemistry, dump combustor flows with n-pentane-air chemistry, nonreacting flow in a model double annular combustor, and nonreacting unsteady driven cavity flows. Numerical results for both the steady and unsteady flows demonstrate the efficiency and robustness of the present algorithm for Mach numbers ranging from the incompressible limit to supersonic speeds.

  20. Chemically Accurate Simulation of a Polyatomic Molecule-Metal Surface Reaction

    PubMed Central

    2016-01-01

    Although important to heterogeneous catalysis, the ability to accurately model reactions of polyatomic molecules with metal surfaces has not kept pace with developments in gas phase dynamics. Partnering the specific reaction parameter (SRP) approach to density functional theory with ab initio molecular dynamics (AIMD) extends our ability to model reactions with metals with quantitative accuracy from only the lightest reactant, H2, to essentially all molecules. This is demonstrated with AIMD calculations on CHD3 + Ni(111) in which the SRP functional is fitted to supersonic beam experiments, and validated by showing that AIMD with the resulting functional reproduces initial-state selected sticking measurements with chemical accuracy (4.2 kJ/mol ≈ 1 kcal/mol). The need for only semilocal exchange makes our scheme computationally tractable for dissociation on transition metals. PMID:27284787

  1. Quantum Chemical Topology: Knowledgeable atoms in peptides

    NASA Astrophysics Data System (ADS)

    Popelier, Paul L. A.

    2012-06-01

    The need to improve atomistic biomolecular force fields remains acute. Fortunately, the abundance of contemporary computing power enables an overhaul of the architecture of current force fields, which typically base their electrostatics on fixed atomic partial charges. We discuss the principles behind the electrostatics of a more realistic force field under construction, called QCTFF. At the heart of QCTFF lies the so-called topological atom, which is a malleable box, whose shape and electrostatics changes in response to a changing environment. This response is captured by a machine learning method called Kriging. Kriging directly predicts each multipole moment of a given atom (i.e. the output) from the coordinates of the nuclei surrounding this atom (i.e. the input). This procedure yields accurate interatomic electrostatic energies, which form the basis for future-proof progress in force field design.

  2. Quantum chemical modeling of rhodopsin mutants displaying switchable colors.

    PubMed

    Melaccio, Federico; Ferré, Nicolas; Olivucci, Massimo

    2012-09-28

    We look at the possibility to compute and understand the color change occurring upon mutation of a photochromic protein. Accordingly, ab initio multiconfigurational quantum chemical methods are used to construct basic quantum-mechanics/molecular-mechanics (QM/MM) models for a small mutant library of the sensory rhodopsin of Anabaena (Nostoc) sp. PCC7120 cyanobacterium. Together with the wild-type forms, a set of 26 absorption maxima spanning a ca. 80 nm range is obtained. We show that these models can be used to capture the electrostatic change controlling the computed color variation and the change in the ionization of specific side chains. PMID:22699180

  3. On the accurate direct computation of the isothermal compressibility for normal quantum simple fluids: application to quantum hard spheres.

    PubMed

    Sesé, Luis M

    2012-06-28

    A systematic study of the direct computation of the isothermal compressibility of normal quantum fluids is presented by analyzing the solving of the Ornstein-Zernike integral (OZ2) equation for the pair correlations between the path-integral necklace centroids. A number of issues related to the accuracy that can be achieved via this sort of procedure have been addressed, paying particular attention to the finite-N effects and to the definition of significant error bars for the estimates of isothermal compressibilities. Extensive path-integral Monte Carlo computations for the quantum hard-sphere fluid (QHS) have been performed in the (N, V, T) ensemble under temperature and density conditions for which dispersion effects dominate the quantum behavior. These computations have served to obtain the centroid correlations, which have been processed further via the numerical solving of the OZ2 equation. To do so, Baxter-Dixon-Hutchinson's variational procedure, complemented with Baumketner-Hiwatari's grand-canonical corrections, has been used. The virial equation of state has also been obtained and several comparisons between different versions of the QHS equation of state have been made. The results show the reliability of the procedure based on isothermal compressibilities discussed herein, which can then be regarded as a useful and quick means of obtaining the equation of state for fluids under quantum conditions involving strong repulsive interactions.

  4. Mapping the chemical potential landscape of a triple quantum dot

    NASA Astrophysics Data System (ADS)

    Broome, M. A.; Gorman, S. K.; Keizer, J. G.; Watson, T. F.; Hile, S. J.; Baker, W. J.; Simmons, M. Y.

    2016-08-01

    We investigate the nonequilibrium charge dynamics of a triple quantum dot and demonstrate how electron transport through these systems can give rise to nontrivial tunneling paths. Using a real-time charge sensing method, we establish tunneling pathways taken by particular electrons under well-defined electrostatic configurations. We show how these measurements map to the chemical potentials for different charge states across the system. We use a modified Hubbard Hamiltonian to describes the system dynamics and show is reproduces all experimental observations.

  5. Accurate determination of the temperature dependent thermalization coefficient (Q) in InAs/AlAsSb quantum wells

    NASA Astrophysics Data System (ADS)

    Esmaielpour, Hamidreza; Tang, Jinfeng; Whiteside, Vincent R.; Vijeyaragunathan, Sangeetha; Mishima, Tetsuya D.; Santos, Michael B.; Sellers, Ian R.

    2015-03-01

    We present an investigation of hot carriers in InAs/AlAsSb quantum wells as a practical candidate for a hot carrier solar cell absorber. The thermalization coefficient (Q) of the sample is investigated using continuous wave photoluminescence (PL). The Q is accurately determined through transfer matrix calculations of the absorption, analysis of the power density, penetration depth, diffusion, and recombination rates using a combination of simulation and empirical methods. A precise measurement of laser spot size is important in order to determine the absorbed power density. Simulations were performed based on our PL geometry in order to calculate the excitation spot size, which was compared with experiment by measurements using variable diameter pinholes to determine beam radius. Here, these techniques are described, in addition to, the temperature dependent hot carrier dynamics and phonon mediated thermalization coefficient for the InAs/AlAsSb quantum well structure.

  6. Charge transfer, chemical potentials, and the nature of functional groups: answers from quantum chemical topology.

    PubMed

    Pendás, A Martín; Francisco, E; Blanco, M A

    2007-01-01

    We analyze the response of a quantum group within a molecule to charge transfer by using the interacting quantum atoms approach (IQA), an energy partitioning scheme within the quantum theory of atoms in molecules (QTAM). It is shown that this response lies at the core of the concept of the functional group. The manipulation of fractional electron populations is carried out by using distribution functions for the electron number within the quantum basins. Several test systems are studied to show that similar chemical potential groups are characterized by similar energetic behavior upon interaction with other groups. The origin of the empirical additivity rules for group energies in simple hydrocarbons is also investigated. It turns out to rest on the independent saturation of both the self-energies and the interaction energies of the groups as the size of the chain increases. We also show that our results are compatible with the standard group energies of the QTAM.

  7. When do perturbative approaches accurately capture the dynamics of complex quantum systems?

    NASA Astrophysics Data System (ADS)

    Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.

    2016-06-01

    Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model.

  8. When do perturbative approaches accurately capture the dynamics of complex quantum systems?

    PubMed Central

    Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.

    2016-01-01

    Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model. PMID:27335176

  9. Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry

    NASA Astrophysics Data System (ADS)

    Tao, Jianmin; Mo, Yuxiang

    2016-08-01

    Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

  10. Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.

    PubMed

    Tao, Jianmin; Mo, Yuxiang

    2016-08-12

    Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals.

  11. Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.

    PubMed

    Tao, Jianmin; Mo, Yuxiang

    2016-08-12

    Most density functionals have been developed by imposing the known exact constraints on the exchange-correlation energy, or by a fit to a set of properties of selected systems, or by both. However, accurate modeling of the conventional exchange hole presents a great challenge, due to the delocalization of the hole. Making use of the property that the hole can be made localized under a general coordinate transformation, here we derive an exchange hole from the density matrix expansion, while the correlation part is obtained by imposing the low-density limit constraint. From the hole, a semilocal exchange-correlation functional is calculated. Our comprehensive test shows that this functional can achieve remarkable accuracy for diverse properties of molecules, solids, and solid surfaces, substantially improving upon the nonempirical functionals proposed in recent years. Accurate semilocal functionals based on their associated holes are physically appealing and practically useful for developing nonlocal functionals. PMID:27563956

  12. Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

    PubMed

    Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

    2008-01-01

    A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

  13. The Bondons: The Quantum Particles of the Chemical Bond

    PubMed Central

    Putz, Mihai V.

    2010-01-01

    By employing the combined Bohmian quantum formalism with the U(1) and SU(2) gauge transformations of the non-relativistic wave-function and the relativistic spinor, within the Schrödinger and Dirac quantum pictures of electron motions, the existence of the chemical field is revealed along the associate bondon particle B̶ characterized by its mass (mB̶), velocity (vB̶), charge (eB̶), and life-time (tB̶). This is quantized either in ground or excited states of the chemical bond in terms of reduced Planck constant ħ, the bond energy Ebond and length Xbond, respectively. The mass-velocity-charge-time quaternion properties of bondons’ particles were used in discussing various paradigmatic types of chemical bond towards assessing their covalent, multiple bonding, metallic and ionic features. The bondonic picture was completed by discussing the relativistic charge and life-time (the actual zitterbewegung) problem, i.e., showing that the bondon equals the benchmark electronic charge through moving with almost light velocity. It carries negligible, although non-zero, mass in special bonding conditions and towards observable femtosecond life-time as the bonding length increases in the nanosystems and bonding energy decreases according with the bonding length-energy relationship Ebond[kcal/mol]×Xbond[A0]=182019, providing this way the predictive framework in which the B̶ particle may be observed. Finally, its role in establishing the virtual states in Raman scattering was also established. PMID:21151435

  14. Quantum analysis of a bandpass Purcell filter for accurate qubit readout

    NASA Astrophysics Data System (ADS)

    Sete, Eyob A.; Martinis, John M.; Korotkov, Alexander N.

    2015-03-01

    In a circuit QED setup the readout fidelity of a superconducting qubit is partially limited by the qubit relaxation through the resonator into a transmission line, which is also known as the Purcell effect. One way to suppress this effect is to employ a filter, which impedes microwave propagation at the qubit frequency. We present a quantum analysis for the bandpass Purcell filter that was recently realized by E. Jeffrey et al. [1]. Using experimental parameters, we show that the bandpass filter suppresses the qubit relaxation rate by two orders of magnitude while keeping the measurement rate the same. We also show that in the presence of a microwave drive the qubit relaxation rate further decreases with increasing drive strength.

  15. Quantum Dynamics of Vinylidene Photodetachment on an Accurate Global Acetylene-Vinylidene Potential Energy Surface.

    PubMed

    Guo, Lifen; Han, Huixian; Ma, Jianyi; Guo, Hua

    2015-08-01

    Vinylidene is a high-energy isomer of acetylene, and the rearrangement of bonds in the two species serves as a prototype for isomerization reactions. Here, a full-dimensional quantum mechanical study of the vinylidene vibration is carried out on a recently developed global acetylene-vinylidene potential energy surface by simulating the photodetachment dynamics of the vinylidene anion. Several low-lying vibrational levels of the anion were first determined on a new ab initio based potential energy surface, and their photoelectron spectra were obtained within the Condon approximation. The vibrational features of the vinylidene isomer are found to agree well with the experiment in both positions and intensities, validating the global acetylene-vinylidene potential energy surface.

  16. Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces

    PubMed Central

    Madebene, Bruno; Ulusoy, Inga; Mancera, Luis; Scribano, Yohann; Chulkov, Sergey

    2011-01-01

    Summary We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters. PMID:22003450

  17. State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation

    PubMed Central

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-01-01

    The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEG), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of 1) the birth and death model, 2) the single gene expression model, 3) the genetic toggle switch model, and 4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate out theories. Overall, the novel state space

  18. State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation.

    PubMed

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-04-01

    The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space

  19. Recommendations for accurate heat capacity measurements using a Quantum Design physical property measurement system

    NASA Astrophysics Data System (ADS)

    Kennedy, Catherine A.; Stancescu, Maria; Marriott, Robert A.; White, Mary Anne

    2007-02-01

    A commercial instrument for determination of heat capacities of solids from ca. 400 K to 0.4 K, the physical property measurement system from Quantum Design, has been used to determine the heat capacities of a standard samples (sapphire [single crystal] and copper). We extend previous tests of the PPMS in three important ways: to temperatures as low as 0.4 K; to samples with poor thermal conductivity; to compare uncertainty with accuracy. We find that the accuracy of heat capacity determinations can be within 1% for 5 K < T < 300 K and 5% for 0.7 K < T < 5 K. Careful attention should be paid to the relative uncertainty for each data point, as determined from multiple measurements. While we have found that it is possible in some circumstances to obtain excellent results by measurement of samples that contribute more than ca. 1/3 to the total heat capacity, there is no "ideal" sample mass and sample geometry also is an important consideration. In fact, our studies of pressed pellets of zirconium tungstate, a poor thermal conductor, show that several samples of different masses should be determined for the highest degree of certainty.

  20. Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations.

    PubMed

    Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

    2015-03-14

    Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online. PMID:25770527

  1. Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

    SciTech Connect

    Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

    2015-03-14

    Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10{sup 3}-10{sup 5} molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

  2. Accurate quantum dynamics calculations using symmetrized Gaussians on a doubly dense Von Neumann lattice

    SciTech Connect

    Halverson, Thomas; Poirier, Bill

    2012-12-14

    In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003); B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004); and ibid. 121, 1704 (2004)], a new method was introduced for performing exact quantum dynamics calculations. The method uses a 'weylet' basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality-the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions).

  3. Accurate quantum thermal rate constants for the three-dimensional H+H2 reaction

    NASA Astrophysics Data System (ADS)

    Park, Tae Jun; Light, J. C.

    1989-07-01

    The rate constants for the three-dimensional H+H2 reaction on the Liu-Siegbahn-Truhlar-Horowitz (LSTH) surface are calculated using Pack-Parker hyperspherical (APH) coordinates and a C2v symmetry adapted direct product discrete variable representation (DVR). The C2v symmetry decomposition and the parity decoupling on the basis are performed for the internal coordinate χ. The symmetry decomposition results in a block diagonal representation of the flux and Hamiltonian operators. The multisurface flux is introduced to represent the multichannel reactive flux. The eigenvalues and eigenvectors of the J=0 internal Hamiltonian are obtained by sequential diagonalization and truncation. The individual symmetry blocks of the flux operator are propagated by the corresponding blocks of the Hamiltonian, and the J=0 rate constant k0(T) is obtained as a sum of the rate constants calculated for each block. k0(T) is compared with the exact k0(T) obtained from thermal averaging of the J=0 reaction probabilities; the errors are within 5%-20% up to T=1500 K. The sequential diagonalization-truncation method reduces the size of the Hamiltonian greatly, but the resulting Hamiltonian matrix still describes the time evolution very accurately. For the J≠0 rate constant calculations, the truncated internal Hamiltonian eigenvector basis is used to construct reduced (JKJ) blocks of the Hamiltonian. The individual (JKJ) blocks are diagonalized neglecting Coriolis coupling and treating the off-diagonal KJ±2 couplings by second order perturbation theory. The full wave function is parity decoupled. The rate constant is obtained as a sum over J of (2J+1)kJ(T). The time evolution of the flux for J≠0 is again very accurately described to give a well converged rate constant.

  4. Quantum-chemical foundations of the topological substructural molecular design.

    PubMed

    Estrada, Ernesto

    2008-06-12

    The topological substructural molecular design (TOPS-MODE) approach is formulated as a tight-binding quantum-chemical method. The approach is based on certain postulates that permit to express any molecular property as a function of the spectral moments of certain types of molecular and environment-dependent energies. We use several empirical potentials to account for these intrinsic and external molecular energies. We prove that any molecular property expressed in terms of a quantitative structure-property and structure-activity relationships (QSPR/QSAR) model developed by using the TOPS-MODE method can be expressed as a bond additivity function. In addition, such a property can also be expressed as a substructural cluster expansion function. The conditions for such bond contributions being transferable are also analyzed here. Several new statistical-mechanical electronic functions are introduced as well as a bond-bond thermal Green's function or a propagator accounting for the electronic hopping between pairs of bonds. All these new concepts are applied to the development and application of a new QSAR model for describing the toxicity of polyhalogenated-dibenzo-1,4-dioxins. The QSAR model obtained displays a significant robustness and predictability. It permits an easy structural interpretation of the structure-activity relationship in terms of bond additivity functions, which display some resemblances with other theoretical parameters obtained from first principle quantum-chemical methods.

  5. A new extension of the polarizable continuum model: Toward a quantum chemical description of chemical reactions at extreme high pressure.

    PubMed

    Cammi, Roberto

    2015-11-15

    A quantum chemical method for studying potential energy surfaces of reactive molecular systems at extreme high pressures is presented. The method is an extension of the standard Polarizable Continuum Model that is usually used for Quantum Chemical study of chemical reactions at a standard condition of pressure. The physical basis of the method and the corresponding computational protocol are described in necessary detail, and an application of the method to the dimerization of cyclopentadiene (up to 20 GPa) is reported.

  6. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    NASA Astrophysics Data System (ADS)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

  7. Chemical dependency in women. Meeting the challenges of accurate diagnosis and effective treatment.

    PubMed Central

    Unger, K B

    1988-01-01

    Women dependent on alcohol or prescribed or nonprescribed psychoactive drugs present special diagnostic challenges to physicians. Chemical dependency likewise has adverse effects on women who are nonusers through the disease of co-dependency. The natural history of chemical dependency in women includes sex-specific differences in presenting signs and symptoms. Collateral medical history may come from a variety of community sources. Diagnoses may also use sex-specific criteria, with simultaneous diagnoses of chemical dependency and co-dependency considered. Images PMID:3074575

  8. Radiation and quantum chemical studies of chalcone derivatives.

    PubMed

    Gaikwad, P; Priyadarsini, K I; Naumov, S; Rao, B S M

    2010-08-01

    The reactions of oxidizing radicals ((*)OH, Br(2)(*-), and SO(4)(*-)) with -OH-, -CH(3)-, or -NH(2)-substituted indole chalcones and hydroxy benzenoid chalcones were studied by radiation and quantum chemical methods. The (*)OH radical was found to react by addition at diffusion-controlled rates (k = 1.1-1.7 x 10(10) dm(3) mol(-1) s(-1)), but Br(2)(*-) radical reacted by 2 orders of magnitude lower. Quantum chemical calculations at the B3LYP/6-31+G(d,p) level of theory have shown that the (C2-OH)(*), (C11-OH)(*), and (C10-OH)(*) adducts of the indole chalcones and the (C7-OH)(*) and (C8-OH)(*) adducts of the hydroxy benzenoid chalcones are more stable with DeltaH = -39 to -28 kcal mol(-1) and DeltaG = -32 to -19 kcal mol(-1). This suggests that (*)OH addition to the alpha,beta-unsaturated bond is a major reaction channel in both types of chalcones and is barrierless. The stability and lack of dehydration of the (*)OH adducts arise from two factors: strong frontier orbital interaction due to the low energy gap between interacting orbitals and the negligible Coulombic repulsion due to small absolute values of Mulliken charges. The transient absorption spectrum measured in the (*)OH radical reaction with all the indole chalcone derivatives exhibited a maximum at 390 nm, which is in excellent agreement with the computed value (394 nm). The formation of three phenolic products under steady-state radiolysis is in line with the three stable (*)OH adducts predicted by theory. Independent of the substituent, identical spectra (lambda(max) = 330-360 and approximately 580 nm) were obtained on one-electron oxidation of the three indole chalcones. MO calculations predict the deprotonation from the -NH group is more efficient than from the substituent due to the larger electron density on the N1 atom forming the chalcone indolyl radical. Its reduction potential was determined to be 0.56 V from the ABTS(*-)/ABTS(2-) couple. In benzenoid chalcones, the (*)OH adduct spectrum is

  9. Response to “Accurate Risk-Based Chemical Screening Relies on Robust Exposure Estimates”

    EPA Science Inventory

    This is a correspondence (letter to the editor) with reference to comments by Rudel and Perovich on the article "Integration of Dosimetry, Exposure, and High-Throughput Screening Data in Chemical Toxicity Assessment". Article Reference: SI # 238882

  10. Simulating chemical energies to high precision with fully-scalable quantum algorithms on superconducting qubits

    NASA Astrophysics Data System (ADS)

    O'Malley, Peter; Babbush, Ryan; Kivlichan, Ian; Romero, Jhonathan; McClean, Jarrod; Tranter, Andrew; Barends, Rami; Kelly, Julian; Chen, Yu; Chen, Zijun; Jeffrey, Evan; Fowler, Austin; Megrant, Anthony; Mutus, Josh; Neill, Charles; Quintana, Christopher; Roushan, Pedram; Sank, Daniel; Vainsencher, Amit; Wenner, James; White, Theodore; Love, Peter; Aspuru-Guzik, Alan; Neven, Hartmut; Martinis, John

    Quantum simulations of molecules have the potential to calculate industrially-important chemical parameters beyond the reach of classical methods with relatively modest quantum resources. Recent years have seen dramatic progress both superconducting qubits and quantum chemistry algorithms. Here, we present experimental demonstrations of two fully-scalable algorithms for finding the dissociation energy of hydrogen: the variational quantum eigensolver and iterative phase estimation. This represents the first calculation of a dissociation energy to chemical accuracy with a non-precompiled algorithm. These results show the promise of chemistry as the ``killer app'' for quantum computers, even before the advent of full error-correction.

  11. Characterization of heterocyclic rings through quantum chemical topology.

    PubMed

    Griffiths, Mark Z; Popelier, Paul L A

    2013-07-22

    Five-membered rings are found in a myriad of molecules important in a wide range of areas such as catalysis, nutrition, and drug and agrochemical design. Systematic insight into their largely unexplored chemical space benefits from first principle calculations presented here. This study comprehensively investigates a grand total of 764 different rings, all geometry optimized at the B3LYP/6-311+G(2d,p) level, from the perspective of Quantum Chemical Topology (QCT). For the first time, a 3D space of local topological properties was introduced, in order to characterize rings compactly. This space is called RCP space, after the so-called ring critical point. This space is analogous to BCP space, named after the bond critical point, which compactly and successfully characterizes a chemical bond. The relative positions of the rings in RCP space are determined by the nature of the ring scaffold, such as the heteroatoms within the ring or the number of π-bonds. The summed atomic QCT charges of the five ring atoms revealed five features (number and type of heteroatom, number of π-bonds, substituent and substitution site) that dictate a ring's net charge. Each feature independently contributes toward a ring's net charge. Each substituent has its own distinct and systematic effect on the ring's net charge, irrespective of the ring scaffold. Therefore, this work proves the possibility of designing a ring with specific properties by fine-tuning it through manipulation of these five features.

  12. Quantum chemical studies of photochromic properties of benzoxazine compound

    NASA Astrophysics Data System (ADS)

    Toliautas, Stepas; Sulskus, Juozas; Valkunas, Leonas; Vengris, Mikas

    2012-08-01

    Molecular electronic structure of ground and excited states of a photochromic indolo[2,1-b][1,3]benzoxazine compound incorporating closed-ring system, which opens upon UV light excitation, was studied using various quantum chemical methods. Three local minima of the ground electronic state potential energy surface and related transition states were identified along the path of rotation of 4-nitrophenol group. Additionally, three local minima of the excited electronic states were located. The evaluated transition energy barriers between local ground-state minima nearest to the initial structure of the investigated molecule are less than 2 kBT, making open structures likely to revert to the initial structure by thermalization. Results obtained using ab initio GMC-QDPT method were explored and compared to the widely used TD-DFT and semi-empiric ZINDO methods.

  13. Quantum cascade laser based standoff photoacoustic chemical detection.

    PubMed

    Chen, Xing; Cheng, Liwei; Guo, Dingkai; Kostov, Yordan; Choa, Fow-Sen

    2011-10-10

    Standoff chemical detection with a distance of more than 41 feet using photoacoustic effect and quantum cascade laser (QCL) operated at relatively low power, less than 40 mW, is demonstrated for the first time. The option of using QCL provides the advantages of easy tuning and modulation besides the benefit of compact size, light weight and low power consumption. The standoff detection signal can be calibrated as a function of different parameters such as laser pulse energy, gas vapor concentration and detection distance. The results yield good agreements with theoretical model. Techniques to obtain even longer detection distance and achieve outdoor operations are in the process of implementation and their projection is discussed.

  14. Chemical potential asymmetry and quantum oscillations in insulators

    NASA Astrophysics Data System (ADS)

    Pal, Hridis K.; Piéchon, Frédéric; Fuchs, Jean-Noël; Goerbig, Mark; Montambaux, Gilles

    2016-09-01

    We present a theory of quantum oscillations in insulators that are particle-hole symmetric and nontopological but with arbitrary band dispersion, at both zero and nonzero temperature. At temperatures T less than or comparable to the gap, the dependence of oscillations on T is markedly different from that in metals and depends crucially on the position of the chemical potential μ in the gap. If μ is in the middle of the gap, oscillations do not change with T ; however, if μ is asymmetrically positioned in the gap, surprisingly, oscillations go to zero at a critical value of the inverse field determined by T and μ and then change their phase by π and grow again. Additionally, the temperature dependence is different for quantities derived from the grand canonical potential, such as magnetization and susceptibility, and those derived from the density of states, such as resistivity. However, the nontrivial features arising from asymmetric μ are present in both.

  15. Simulation of Chemical Isomerization Reaction Dynamics on a NMR Quantum Simulator

    NASA Astrophysics Data System (ADS)

    Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-07-01

    Quantum simulation can beat current classical computers with minimally a few tens of qubits. Here we report an experimental demonstration that a small nuclear-magnetic-resonance quantum simulator is already able to simulate the dynamics of a prototype laser-driven isomerization reaction using engineered quantum control pulses. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.

  16. Assessment of quantum-chemical methods for electronic properties and geometry of signaling biomolecules.

    PubMed

    Ferro, Noel; Bredow, Thomas

    2010-04-15

    A reasonable balance between accuracy and feasibility of quantum-chemical methods depends on the complexity of the molecular system and the scientific goals. Six series of indole-, naphthalene-, phenol-, benzoic-, phenoxy-, other auxin-derivatives, and a test set of similar organic molecules have been chosen for an assessment of 13 density functional and semi-empirical molecular orbital methods with respect to electronic and structural properties. The accuracy and precision of HOMO/LUMO calculations are determined by comparison with experimental ionization potentials and electron affinities. Further comparison was performed at atomic level by covariance analysis. The methods KMLYP, MSINDO, and PM3 are precise and accurate for the whole set of molecules. The method AM1 offers comparable accuracy with the exception of electron affinities of indole derivatives, where significant deviations from experiment were observed. Geometrical properties were best reproduced with the semi-empirical method MSINDO. PMID:19899146

  17. Quantum chemical approach for condensed-phase thermochemistry: Proposal of a harmonic solvation model

    SciTech Connect

    Nakai, Hiromi; Ishikawa, Atsushi

    2014-11-07

    We propose a novel quantum chemical method, called the harmonic solvation model (HSM), for calculating thermochemical parameters in the condensed phase, particularly in the liquid phase. The HSM represents translational and rotational motions of a solute as vibrations interacting with a cavity wall of solvent molecules. As examples, the HSM and the ideal-gas model (IGM) were used for the standard formation reaction of liquid water, combustion reactions of liquid formic acid, methanol, and ethanol, vapor–liquid equilibration of water and ethanol, and dissolution of gaseous CO{sub 2} in water. The numerical results confirmed the reliability and applicability of the HSM. In particular, the temperature dependence of the Gibbs energy of liquid molecules was accurately reproduced by the HSM; for example, the boiling point of water was reasonably determined using the HSM, whereas the conventional IGM treatment failed to obtain a crossing of the two Gibbs energy curves for gaseous and liquid water.

  18. Quantum chemical tests of water-water potential for interaction site water models.

    PubMed

    Huš, Matej; Urbič, Tomaž

    2012-09-01

    Accuracy of different simple interaction site water models was tested. Instead of assessing their quality through the calculations of various water physical properties (dipole moment, dielectric constant, phase-equilibria diagrams, etc.) and comparison with experimental values, we calculated water-water potential and compared it with the potential from quantum chemical calculations. Using density functional theory (DFT) water-water potential was calculated for different positions of two water molecules, which was compared with the interaction used in water models. Different simple interaction site water models were then evaluated and assessed. Special emphasis is placed on angle and distance dependence of water-water potential around minima in the potential. Among three-, four-and five-site electrostatic water models, TIP3P, TIP4P/2005 and TIP5P were found to be the most accurate.

  19. Quantum chemical calculations predict biological function: the case of T cell receptor interaction with a peptide/MHC class I

    PubMed Central

    Antipas, Georgios S. E.; Germenis, Anastasios E.

    2015-01-01

    A combination of atomic correlation statistics and quantum chemical calculations are shown to predict biological function. In the present study, various antigenic peptide-Major Histocompatibility Complex (pMHC) ligands with near-identical stereochemistries, in complexation with the same T cell receptor (TCR), were found to consistently induce distinctly different quantum chemical behavior, directly dependent on the peptide's electron spin density and intrinsically expressed by the protonation state of the peptide's N-terminus. Furthermore, the cumulative coordination difference of any variant in respect to the native peptide was found to accurately reflect peptide biological function and immerges as the physical observable which is directly related to the immunological end-effect of pMHC-TCR interaction. PMID:25713797

  20. Quantum chemical calculations predict biological function: The case of T cell receptor interaction with a peptide/MHC class I

    NASA Astrophysics Data System (ADS)

    Antipas, Georgios S. E.; Germenis, Anastasios

    2015-02-01

    A combination of atomic correlation statistics and quantum chemical calculations are shown to predict biological function. In the present study, various antigenic peptide-Major Histocompatibility Complex (pMHC) ligands with near-identical stereochemistries, in complexation with the same T cell receptor (TCR), were found to consistently induce distinctly different quantum chemical behavior, directly dependent on the peptide’s electron spin density and intrinsically expressed by the protonation state of the peptide’s N-terminus. Furthermore, the cumulative coordination difference of any variant in respect to the native peptide was found to accurately reflect peptide biological function and immerges as the physical observable which is directly related to the immunological end-effect of pMHC-TCR interaction.

  1. Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

    NASA Astrophysics Data System (ADS)

    Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

    2016-12-01

    Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

  2. Unconditionally stable, second-order accurate schemes for solid state phase transformations driven by mechano-chemical spinodal decomposition

    DOE PAGES

    Sagiyama, Koki; Rudraraju, Shiva; Garikipati, Krishna

    2016-09-13

    Here, we consider solid state phase transformations that are caused by free energy densities with domains of non-convexity in strain-composition space; we refer to the non-convex domains as mechano-chemical spinodals. The non-convexity with respect to composition and strain causes segregation into phases with different crystal structures. We work on an existing model that couples the classical Cahn-Hilliard model with Toupin’s theory of gradient elasticity at finite strains. Both systems are represented by fourth-order, nonlinear, partial differential equations. The goal of this work is to develop unconditionally stable, second-order accurate time-integration schemes, motivated by the need to carry out large scalemore » computations of dynamically evolving microstructures in three dimensions. We also introduce reduced formulations naturally derived from these proposed schemes for faster computations that are still second-order accurate. Although our method is developed and analyzed here for a specific class of mechano-chemical problems, one can readily apply the same method to develop unconditionally stable, second-order accurate schemes for any problems for which free energy density functions are multivariate polynomials of solution components and component gradients. Apart from an analysis and construction of methods, we present a suite of numerical results that demonstrate the schemes in action.« less

  3. Unconditionally stable, second-order accurate schemes for solid state phase transformations driven by mechano-chemical spinodal decomposition

    NASA Astrophysics Data System (ADS)

    Sagiyama, K.; Rudraraju, S.; Garikipati, K.

    2016-11-01

    We consider solid state phase transformations that are caused by free energy densities with domains of non-convexity in strain-composition space; we refer to the non-convex domains as mechano-chemical spinodals. The non-convexity with respect to composition and strain causes segregation into phases with different crystal structures. We work on an existing model that couples the classical Cahn-Hilliard model with Toupin's theory of gradient elasticity at finite strains. Both systems are represented by fourth-order, nonlinear, partial differential equations. The goal of this work is to develop unconditionally stable, second-order accurate time-integration schemes, motivated by the need to carry out large scale computations of dynamically evolving microstructures in three dimensions. We also introduce reduced formulations naturally derived from these proposed schemes for faster computations that are still second-order accurate. Although our method is developed and analyzed here for a specific class of mechano-chemical problems, one can readily apply the same method to develop unconditionally stable, second-order accurate schemes for any problems for which free energy density functions are multivariate polynomials of solution components and component gradients. Apart from an analysis and construction of methods, we present a suite of numerical results that demonstrate the schemes in action.

  4. An accurate and self-consistent chemical abundance catalogue for the APOGEE/Kepler sample

    NASA Astrophysics Data System (ADS)

    Hawkins, K.; Masseron, T.; Jofré, P.; Gilmore, G.; Elsworth, Y.; Hekker, S.

    2016-10-01

    Context. The APOGEE survey has obtained high-resolution infrared spectra of more than 100 000 stars. Deriving chemical abundances patterns of these stars is paramount to piecing together the structure of the Milky Way. While the derived chemical abundances have been shown to be precise for most stars, some calibration problems have been reported, in particular for more metal-poor stars. Aims: In this paper, we aim to (1) re-determine the chemical abundances of the APOGEE+Kepler stellar sample (APOKASC) with an independent procedure, line list and line selection, and high-quality surface gravity information from asteroseismology; and (2) extend the abundance catalogue by including abundances that are not currently reported in the most recent APOGEE release (DR12). Methods: We fixed the Teff and log g to those determined using spectrophotometric and asteroseismic techniques, respectively. We made use of the Brussels Automatic Stellar Parameter (BACCHUS) code to derive the metallicity and broadening parameters for the APOKASC sample. In addition, we derived differential abundances with respect to Arcturus. Results: We have validated the BACCHUS code on APOGEE data using several well-known stars, and stars from open and globular clusters. We also provide the abundances of C, N, O, Mg, Ca, Si, Ti, S, Al, Na, Ni, Mn, Fe, K, and V for every star and line, and show the impact of line selection on the final abundances. Improvements have been made for some elements (e.g. Ti, Si, V). Additionally, we measure new abundance ratios not found in the current APOGEE release including P, Cu, Rb, and Yb, which are only upper limits at this time, as well as Co and Cr which are promising. Conclusions: In this paper, we present an independent analysis of the APOKASC sample and provide abundances of up to 21 elements. This catalogue can be used not only to study chemical abundance patterns of the Galaxy but also to train data driven spectral approaches which can improve the abundance

  5. The quantum dynamics of electronically nonadiabatic chemical reactions

    NASA Astrophysics Data System (ADS)

    Truhlar, Donald G.

    1993-04-01

    Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally

  6. The quantum dynamics of electronically nonadiabatic chemical reactions

    NASA Technical Reports Server (NTRS)

    Truhlar, Donald G.

    1993-01-01

    Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally

  7. Exploring the role of quantum chemical descriptors in modeling acute toxicity of diverse chemicals to Daphnia magna.

    PubMed

    Reenu; Vikas

    2015-09-01

    Various quantum-mechanically computed molecular and thermodynamic descriptors along with physico-chemical, electrostatic and topological descriptors are compared while developing quantitative structure-activity relationships (QSARs) for the acute toxicity of 252 diverse organic chemicals towards Daphnia magna. QSAR models based on the quantum-chemical descriptors, computed with routinely employed advanced semi-empirical and ab-initio methods, along with the electron-correlation contribution (CORR) of the descriptors, are analyzed for the external predictivity of the acute toxicity. The models with reliable internal stability and external predictivity are found to be based on the HOMO energy along with the physico-chemical, electrostatic and topological descriptors. Besides this, the total energy and electron-correlation energy are also observed as highly reliable descriptors, suggesting that the intra-molecular interactions between the electrons play an important role in the origin of the acute toxicity, which is in fact an unexplored phenomenon. The models based on quantum-chemical descriptors such as chemical hardness, absolute electronegativity, standard Gibbs free energy and enthalpy are also observed to be reliable. A comparison of the robust models based on the quantum-chemical descriptors computed with various quantum-mechanical methods suggests that the advanced semi-empirical methods such as PM7 can be more reliable than the ab-initio methods which are computationally more expensive.

  8. Exploring the role of quantum chemical descriptors in modeling acute toxicity of diverse chemicals to Daphnia magna.

    PubMed

    Reenu; Vikas

    2015-09-01

    Various quantum-mechanically computed molecular and thermodynamic descriptors along with physico-chemical, electrostatic and topological descriptors are compared while developing quantitative structure-activity relationships (QSARs) for the acute toxicity of 252 diverse organic chemicals towards Daphnia magna. QSAR models based on the quantum-chemical descriptors, computed with routinely employed advanced semi-empirical and ab-initio methods, along with the electron-correlation contribution (CORR) of the descriptors, are analyzed for the external predictivity of the acute toxicity. The models with reliable internal stability and external predictivity are found to be based on the HOMO energy along with the physico-chemical, electrostatic and topological descriptors. Besides this, the total energy and electron-correlation energy are also observed as highly reliable descriptors, suggesting that the intra-molecular interactions between the electrons play an important role in the origin of the acute toxicity, which is in fact an unexplored phenomenon. The models based on quantum-chemical descriptors such as chemical hardness, absolute electronegativity, standard Gibbs free energy and enthalpy are also observed to be reliable. A comparison of the robust models based on the quantum-chemical descriptors computed with various quantum-mechanical methods suggests that the advanced semi-empirical methods such as PM7 can be more reliable than the ab-initio methods which are computationally more expensive. PMID:26188798

  9. Chemical physics: Quantum control of light-induced reactions

    NASA Astrophysics Data System (ADS)

    Chandler, David W.

    2016-07-01

    An investigation of how ultracold molecules are broken apart by light reveals surprising, previously unobserved quantum effects. The work opens up avenues of research in quantum optics. See Letter p.122

  10. Small pores in soils: Is the physico-chemical environment accurately reflected in biogeochemical models ?

    NASA Astrophysics Data System (ADS)

    Weber, Tobias K. D.; Riedel, Thomas

    2015-04-01

    Free water is a prerequesite to chemical reactions and biological activity in earth's upper crust essential to life. The void volume between the solid compounds provides space for water, air, and organisms that thrive on the consumption of minerals and organic matter thereby regulating soil carbon turnover. However, not all water in the pore space in soils and sediments is in its liquid state. This is a result of the adhesive forces which reduce the water activity in small pores and charged mineral surfaces. This water has a lower tendency to react chemically in solution as this additional binding energy lowers its activity. In this work, we estimated the amount of soil pore water that is thermodynamically different from a simple aqueous solution. The quantity of soil pore water with properties different to liquid water was found to systematically increase with increasing clay content. The significance of this is that the grain size and surface area apparently affects the thermodynamic state of water. This implies that current methods to determine the amount of water content, traditionally determined from bulk density or gravimetric water content after drying at 105°C overestimates the amount of free water in a soil especially at higher clay content. Our findings have consequences for biogeochemical processes in soils, e.g. nutrients may be contained in water which is not free which could enhance preservation. From water activity measurements on a set of various soils with 0 to 100 wt-% clay, we can show that 5 to 130 mg H2O per g of soil can generally be considered as unsuitable for microbial respiration. These results may therefore provide a unifying explanation for the grain size dependency of organic matter preservation in sedimentary environments and call for a revised view on the biogeochemical environment in soils and sediments. This could allow a different type of process oriented modelling.

  11. Quantum Hall resistance standards from graphene grown by chemical vapour deposition on silicon carbide

    PubMed Central

    Lafont, F.; Ribeiro-Palau, R.; Kazazis, D.; Michon, A.; Couturaud, O.; Consejo, C.; Chassagne, T.; Zielinski, M.; Portail, M.; Jouault, B.; Schopfer, F.; Poirier, W.

    2015-01-01

    Replacing GaAs by graphene to realize more practical quantum Hall resistance standards (QHRS), accurate to within 10−9 in relative value, but operating at lower magnetic fields than 10 T, is an ongoing goal in metrology. To date, the required accuracy has been reported, only few times, in graphene grown on SiC by Si sublimation, under higher magnetic fields. Here, we report on a graphene device grown by chemical vapour deposition on SiC, which demonstrates such accuracies of the Hall resistance from 10 T up to 19 T at 1.4 K. This is explained by a quantum Hall effect with low dissipation, resulting from strongly localized bulk states at the magnetic length scale, over a wide magnetic field range. Our results show that graphene-based QHRS can replace their GaAs counterparts by operating in as-convenient cryomagnetic conditions, but over an extended magnetic field range. They rely on a promising hybrid and scalable growth method and a fabrication process achieving low-electron-density devices. PMID:25891533

  12. [Study of quantum-pharmacological chemical characteristics of quercetin].

    PubMed

    Zahorodnyĭ, M I

    2007-01-01

    It was established in the previous studies that quercetin prevented the development and caused faster regression of ulcers, petechia and anabroses in rats, which were induced by diclofenac taking. In the group of patients taking diclofenac together with quercetin, the ulcers and dyspeptic events were less found. The application of quercetin normalizes the function and metabolism of cartilage tissue of rabbits with an experimental osteoarthrosis and in patients with osteoartrosis. Quantum-chemical properties of molecule quercetin were studied using the methods of molecular mechanics MM+ and ab initio 6-31G*, and also semiempirical method. The following indices were investigated: distance between atoms (A), the distribution of electronic density of only external valency electrons, distribution of electrostatic potential; common energy of the exertion of molecule (kkal/mmol); binding energy (kkal/mmol); electron energy (kkal/mmol); energy of nucleus-nucleus interaction (kkal/mmol); formation heat (kkal/mmol); atomic charge (eB); value of the dipole moment of molecule (D); localization and energy of highest occupied orbital (HOMO) and the lowest unoccupied (LUMO) molecular orbital (eB) of quercetin miolecule; the value of absolute rigidity of chemical structure of bioflavonoid. It was shown, that bioflavonoid quercetin belongs to mild reagents, has nucleophilic properties, can react with alkaline, unsaturated and aromatic compounds,. Polar substitutes in the quercetine molecule influence on the distribution of superficial valency electrons and localization of HOMO and LUMO. The energy value of quercetin LUMO enables us to refer quercetine to the reducing agent and it is illustrated by antioxidant properties of this medicine. PMID:18663944

  13. New insights for accurate chemically specific measurements of slow diffusing molecules.

    PubMed

    Hou, Jianbo; Madsen, Louis A

    2013-02-01

    Investigating the myriad features of molecular transport in materials yields fundamental information for understanding processes such as ion conduction, chemical reactions, and phase transitions. Molecular transport especially impacts the performance of ion-containing liquids and polymeric materials when used as electrolytes and separation media, with applications encompassing battery electrolytes, reverse-osmosis membranes, mechanical transducers, and fuel cells. Nuclear magnetic resonance (NMR) provides a unique probe of molecular translations by allowing measurement of all mobile species via spectral selectivity, access to a broad range of transport coefficients, probing of any material direction, and investigation of variable lengthscales in a material, thus, tying morphology to transport. Here, we present new concepts to test for and guarantee robust diffusion measurements. We first employ a standard pulsed-field-gradient (PFG) calibration protocol using (2)H(2)O and obtain expected results, but we observe crippling artifacts when measuring (1)H-glycerol diffusion with the same experimental parameters. A mathematical analysis of (2)H(2)O and glycerol signals in the presence of PFG transients show tight agreement with experimental observations. These analyses lead to our principal findings that (1) negligible artifacts observed with low gyromagnetic ratio (γ) nuclei may become dominant when observing high γ nuclei, and (2) reducing the sample dimension along the gradient direction predictably reduces non-ideal behaviors of NMR signals. We further provide a useful quantitative strategy for error minimization when measuring diffusing species slower than the one used for gradient calibration. PMID:23406112

  14. New insights for accurate chemically specific measurements of slow diffusing molecules

    NASA Astrophysics Data System (ADS)

    Hou, Jianbo; Madsen, Louis A.

    2013-02-01

    Investigating the myriad features of molecular transport in materials yields fundamental information for understanding processes such as ion conduction, chemical reactions, and phase transitions. Molecular transport especially impacts the performance of ion-containing liquids and polymeric materials when used as electrolytes and separation media, with applications encompassing battery electrolytes, reverse-osmosis membranes, mechanical transducers, and fuel cells. Nuclear magnetic resonance (NMR) provides a unique probe of molecular translations by allowing measurement of all mobile species via spectral selectivity, access to a broad range of transport coefficients, probing of any material direction, and investigation of variable lengthscales in a material, thus, tying morphology to transport. Here, we present new concepts to test for and guarantee robust diffusion measurements. We first employ a standard pulsed-field-gradient (PFG) calibration protocol using 2H2O and obtain expected results, but we observe crippling artifacts when measuring 1H-glycerol diffusion with the same experimental parameters. A mathematical analysis of 2H2O and glycerol signals in the presence of PFG transients show tight agreement with experimental observations. These analyses lead to our principal findings that (1) negligible artifacts observed with low gyromagnetic ratio (γ) nuclei may become dominant when observing high γ nuclei, and (2) reducing the sample dimension along the gradient direction predictably reduces non-ideal behaviors of NMR signals. We further provide a useful quantitative strategy for error minimization when measuring diffusing species slower than the one used for gradient calibration.

  15. Detection of chemical clouds using widely tunable quantum cascade lasers

    NASA Astrophysics Data System (ADS)

    Goyal, Anish K.; Kotidis, Petros; Deutsch, Erik R.; Zhu, Ninghui; Norman, Mark; Ye, Jim; Zafiriou, Kostas; Mazurenko, Alexander

    2015-05-01

    Widely tunable quantum cascade lasers (QCLs) spanning the long-wave infrared (LWIR) atmospheric transmission window and an HgCdTe detector were incorporated into a transceiver having a 50-mm-diameter transmit/receive aperture. The transceiver was used in combination with a 50-mm-diameter hollow retro-reflector for the open-path detection of chemical clouds. Two rapidly tunable external-cavity QCLs spanned the wavelength range of 7.5 to 12.8 m. Open-path transmission measurements were made over round-trip path-lengths of up to 562 meters. Freon-132a and other gases were sprayed into the beam path and the concentration-length (CL) product was measured as a function of time. The system exhibited a noise-equivalent concentration (NEC) of 3 ppb for Freon-132a given a round-trip path of 310 meters. Algorithms based on correlation methods were used to both identify the gases and determine their CLproducts as a function of time.

  16. Microsolvation of methyl hydrogen peroxide: Ab initio quantum chemical approach

    NASA Astrophysics Data System (ADS)

    Kulkarni, Anant D.; Rai, Dhurba; Bartolotti, Libero J.; Pathak, Rajeev K.

    2009-08-01

    Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP⋯(H2O)n, [n =1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP⋯(H2O)8. Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.

  17. Comparison of sugar molecule decomposition through glucose and fructose: a high-level quantum chemical study.

    SciTech Connect

    Assary, R. S.; Curtiss, L. A.

    2012-02-01

    Efficient chemical conversion of biomass is essential to produce sustainable energy and industrial chemicals. Industrial level conversion of glucose to useful chemicals, such as furfural, hydroxymethylfurfural, and levulinic acid, is a major step in the biomass conversion but is difficult because of the formation of undesired products and side reactions. To understand the molecular level reaction mechanisms involved in the decomposition of glucose and fructose, we have carried out high-level quantum chemical calculations [Gaussian-4 (G4) theory]. Selective 1,2-dehydration, keto-enol tautomerization, isomerization, retro-aldol condensation, and hydride shifts of glucose and fructose molecules were investigated. Detailed kinetic and thermodynamic analyses indicate that, for acyclic glucose and fructose molecules, the dehydration and isomerization require larger activation barriers compared to the retro-aldol reaction at 298 K in neutral medium. The retro-aldol reaction results in the formation of C2 and C4 species from glucose and C3 species from fructose. The formation of the most stable C3 species, dihydroxyacetone from fructose, is thermodynamically downhill. The 1,3-hydride shift leads to the cleavage of the C-C bond in the acyclic species; however, the enthalpy of activation is significantly higher (50-55 kcal/mol) than that of the retro-aldol reaction (38 kcal/mol) mainly because of the sterically hindered distorted four-membered transition state compared to the hexa-membered transition state in the retro-aldol reaction. Both tautomerization and dehydration are catalyzed by a water molecule in aqueous medium; however, water has little effect on the retro-aldol reaction. Isomerization of glucose to fructose and glyceraldehyde to dihydroxyacetone proceeds through hydride shifts that require an activation enthalpy of about 40 kcal/mol at 298 K in water medium. This investigation maps out accurate energetics of the decomposition of glucose and fructose molecules

  18. Chemical Compass Model for Avian Magnetoreception as a Quantum Coherent Device

    NASA Astrophysics Data System (ADS)

    Cai, Jianming; Plenio, Martin B.

    2013-12-01

    It is known that more than 50 species use the Earth’s magnetic field for orientation and navigation. Intensive studies, particularly behavior experiments with birds, provide support for a chemical compass based on magnetically sensitive free radical reactions as a source of this sense. However, the fundamental question of how quantum coherence plays an essential role in such a chemical compass model of avian magnetoreception yet remains controversial. Here, we show that the essence of the chemical compass model can be understood in analogy to a quantum interferometer exploiting global quantum coherence rather than any subsystem coherence. Within the framework of quantum metrology, we quantify global quantum coherence and correlate it with the function of chemical magnetoreception. Our results allow us to understand and predict how various factors can affect the performance of a chemical compass from the unique perspective of quantum coherence assisted metrology. This represents a crucial step to affirm a direct connection between quantum coherence and the function of a chemical compass.

  19. Chemical compass model for avian magnetoreception as a quantum coherent device.

    PubMed

    Cai, Jianming; Plenio, Martin B

    2013-12-01

    It is known that more than 50 species use the Earth's magnetic field for orientation and navigation. Intensive studies, particularly behavior experiments with birds, provide support for a chemical compass based on magnetically sensitive free radical reactions as a source of this sense. However, the fundamental question of how quantum coherence plays an essential role in such a chemical compass model of avian magnetoreception yet remains controversial. Here, we show that the essence of the chemical compass model can be understood in analogy to a quantum interferometer exploiting global quantum coherence rather than any subsystem coherence. Within the framework of quantum metrology, we quantify global quantum coherence and correlate it with the function of chemical magnetoreception. Our results allow us to understand and predict how various factors can affect the performance of a chemical compass from the unique perspective of quantum coherence assisted metrology. This represents a crucial step to affirm a direct connection between quantum coherence and the function of a chemical compass. PMID:24476240

  20. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.

    PubMed

    Šponer, Jiří; Šponer, Judit E; Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal

    2013-11-01

    In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments.

  1. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.

    PubMed

    Šponer, Jiří; Šponer, Judit E; Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal

    2013-11-01

    In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments. PMID:23747334

  2. A guide to accurate measurement of diffusion using fluorescence correlation techniques with blinking quantum dot nanoparticle labels.

    PubMed

    Bachir, Alexia I; Kolin, David L; Heinze, Katrin G; Hebert, Benedict; Wiseman, Paul W

    2008-06-14

    Fluctuation-based fluorescence correlation techniques are widely used to study dynamics of fluorophore labeled biomolecules in cells. Semiconductor quantum dots (QDs) have been developed as bright and photostable fluorescent probes for various biological applications. However, the fluorescence intermittency of QDs, commonly referred to as "blinking", is believed to complicate quantitative correlation spectroscopy measurements of transport properties, as it is an additional source of fluctuations that contribute on a wide range of time scales. The QD blinking fluctuations obey power-law distributions so there is no single characteristic fluctuation time for this phenomenon. Consequently, it is highly challenging to separate fluorescence blinking fluctuations from those due to transport dynamics. Here, we quantify the bias introduced by QD blinking in transport measurements made using fluctuation methods. Using computer simulated image time series of diffusing point emitters with set "on" and "off" time emission characteristics, we show that blinking results in a systematic overestimation of the diffusion coefficients measured with correlation analysis when a simple diffusion model is used to fit the time correlation decays. The relative error depends on the inherent blinking power-law statistics, the sampling rate relative to the characteristic diffusion time and blinking times, and the total number of images in the time series. This systematic error can be significant; moreover, it can often go unnoticed in common transport model fits of experimental data. We propose an alternative fitting model that incorporates blinking and improves the accuracy of the recovered diffusion coefficients. We also show how to completely eliminate the bias by applying k-space image correlation spectroscopy, which completely separates the diffusion and blinking dynamics, and allows the simultaneous recovery of accurate diffusion coefficients and QD blinking probability distribution

  3. Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining.

    PubMed

    Wedler, Henry B; Pemberton, Ryan P; Lounnas, Valère; Vriend, Gert; Tantillo, Dean J; Wang, Selina C

    2015-05-01

    Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined.

  4. Optimization of an External Cavity Quantum Cascade Laser for Chemical Sensing Applications

    SciTech Connect

    Phillips, Mark C.; Bernacki, Bruce E.; Taubman, Matthew S.; Cannon, Bret D.; Schiffern, John T.; Myers, Tanya L.

    2010-03-01

    We describe and characterize an external cavity quantum cascade laser designed for detection of multiple airborne chemicals, and used with a compact astigmatic Herriott cell for sensing of acetone and hydrogen peroxide.

  5. Spectroscopic and quantum chemical analysis of Isonicotinic acid methyl ester

    NASA Astrophysics Data System (ADS)

    Shoba, D.; Periandy, S.; Govindarajan, M.; Gayathri, P.

    2015-02-01

    In this present study, an organic compound Isonicotinic acid methyl ester (INAME) was structurally characterized by FTIR, FT-Raman, and NMR and UV spectroscopy. The optimized geometrical parameters and energies of all different and possible conformers of INAME are obtained from Density Functional Theory (DFT) by B3LYP/6-311++G(d,p) method. There are three conformers (SI, SII-1, and SII-2) for this molecule (ground state). The most stable conformer of INAME is SI conformer. The molecular geometry and vibrational frequencies of INAME in the ground state have been calculated by using HF and density functional method (B3LYP) 6-311++G (d,p) basis set. Detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The computed vibrational frequencies were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. A study on the electronic properties, such as HOMO and LUMO energies were performed by time independent DFT approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and first hyper polarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results show that the INAME molecule may have microscopic nonlinear optical (NLO) behavior with non zero values. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by gauge independent atomic orbital (GIAO) method.

  6. Fast infrared chemical imaging with a quantum cascade laser.

    PubMed

    Yeh, Kevin; Kenkel, Seth; Liu, Jui-Nung; Bhargava, Rohit

    2015-01-01

    Infrared (IR) spectroscopic imaging systems are a powerful tool for visualizing molecular microstructure of a sample without the need for dyes or stains. Table-top Fourier transform infrared (FT-IR) imaging spectrometers, the current established technology, can record broadband spectral data efficiently but requires scanning the entire spectrum with a low throughput source. The advent of high-intensity, broadly tunable quantum cascade lasers (QCL) has now accelerated IR imaging but results in a fundamentally different type of instrument and approach, namely, discrete frequency IR (DF-IR) spectral imaging. While the higher intensity of the source provides a higher signal per channel, the absence of spectral multiplexing also provides new opportunities and challenges. Here, we couple a rapidly tunable QCL with a high performance microscope equipped with a cooled focal plane array (FPA) detector. Our optical system is conceptualized to provide optimal performance based on recent theory and design rules for high-definition (HD) IR imaging. Multiple QCL units are multiplexed together to provide spectral coverage across the fingerprint region (776.9 to 1904.4 cm(-1)) in our DF-IR microscope capable of broad spectral coverage, wide-field detection, and diffraction-limited spectral imaging. We demonstrate that the spectral and spatial fidelity of this system is at least as good as the best FT-IR imaging systems. Our configuration provides a speedup for equivalent spectral signal-to-noise ratio (SNR) compared to the best spectral quality from a high-performance linear array system that has 10-fold larger pixels. Compared to the fastest available HD FT-IR imaging system, we demonstrate scanning of large tissue microarrays (TMA) in 3-orders of magnitude smaller time per essential spectral frequency. These advances offer new opportunities for high throughput IR chemical imaging, especially for the measurement of cells and tissues.

  7. Fast Infrared Chemical Imaging with a Quantum Cascade Laser

    PubMed Central

    2015-01-01

    Infrared (IR) spectroscopic imaging systems are a powerful tool for visualizing molecular microstructure of a sample without the need for dyes or stains. Table-top Fourier transform infrared (FT-IR) imaging spectrometers, the current established technology, can record broadband spectral data efficiently but requires scanning the entire spectrum with a low throughput source. The advent of high-intensity, broadly tunable quantum cascade lasers (QCL) has now accelerated IR imaging but results in a fundamentally different type of instrument and approach, namely, discrete frequency IR (DF-IR) spectral imaging. While the higher intensity of the source provides a higher signal per channel, the absence of spectral multiplexing also provides new opportunities and challenges. Here, we couple a rapidly tunable QCL with a high performance microscope equipped with a cooled focal plane array (FPA) detector. Our optical system is conceptualized to provide optimal performance based on recent theory and design rules for high-definition (HD) IR imaging. Multiple QCL units are multiplexed together to provide spectral coverage across the fingerprint region (776.9 to 1904.4 cm–1) in our DF-IR microscope capable of broad spectral coverage, wide-field detection, and diffraction-limited spectral imaging. We demonstrate that the spectral and spatial fidelity of this system is at least as good as the best FT-IR imaging systems. Our configuration provides a speedup for equivalent spectral signal-to-noise ratio (SNR) compared to the best spectral quality from a high-performance linear array system that has 10-fold larger pixels. Compared to the fastest available HD FT-IR imaging system, we demonstrate scanning of large tissue microarrays (TMA) in 3-orders of magnitude smaller time per essential spectral frequency. These advances offer new opportunities for high throughput IR chemical imaging, especially for the measurement of cells and tissues. PMID:25474546

  8. Fast infrared chemical imaging with a quantum cascade laser.

    PubMed

    Yeh, Kevin; Kenkel, Seth; Liu, Jui-Nung; Bhargava, Rohit

    2015-01-01

    Infrared (IR) spectroscopic imaging systems are a powerful tool for visualizing molecular microstructure of a sample without the need for dyes or stains. Table-top Fourier transform infrared (FT-IR) imaging spectrometers, the current established technology, can record broadband spectral data efficiently but requires scanning the entire spectrum with a low throughput source. The advent of high-intensity, broadly tunable quantum cascade lasers (QCL) has now accelerated IR imaging but results in a fundamentally different type of instrument and approach, namely, discrete frequency IR (DF-IR) spectral imaging. While the higher intensity of the source provides a higher signal per channel, the absence of spectral multiplexing also provides new opportunities and challenges. Here, we couple a rapidly tunable QCL with a high performance microscope equipped with a cooled focal plane array (FPA) detector. Our optical system is conceptualized to provide optimal performance based on recent theory and design rules for high-definition (HD) IR imaging. Multiple QCL units are multiplexed together to provide spectral coverage across the fingerprint region (776.9 to 1904.4 cm(-1)) in our DF-IR microscope capable of broad spectral coverage, wide-field detection, and diffraction-limited spectral imaging. We demonstrate that the spectral and spatial fidelity of this system is at least as good as the best FT-IR imaging systems. Our configuration provides a speedup for equivalent spectral signal-to-noise ratio (SNR) compared to the best spectral quality from a high-performance linear array system that has 10-fold larger pixels. Compared to the fastest available HD FT-IR imaging system, we demonstrate scanning of large tissue microarrays (TMA) in 3-orders of magnitude smaller time per essential spectral frequency. These advances offer new opportunities for high throughput IR chemical imaging, especially for the measurement of cells and tissues. PMID:25474546

  9. GaN quantum dots as optical transducers for chemical sensors

    SciTech Connect

    Weidemann, O.; Jegert, G.; Stutzmann, M.; Kandaswamy, P. K.; Monroy, E.

    2009-03-16

    GaN/AlN quantum dots were investigated as optical transducers for field effect chemical sensors. The structures were synthesized by molecular-beam epitaxy and covered by a semitransparent catalytic Pt top contact. Due to the thin (3 nm) AlN barriers, the variation of the quantum dot photoluminescence with an external electric field along the [0001] axis is dominated by the tunneling current rather than by the quantum confined Stark effect. An increasing field results in a blueshift of the luminescence and a decreasing intensity. This effect is used to measure the optical response of quantum dot superlattices upon exposure to molecular hydrogen.

  10. Quantum chemical modeling of zeolite-catalyzed methylation reactions: toward chemical accuracy for barriers.

    PubMed

    Svelle, Stian; Tuma, Christian; Rozanska, Xavier; Kerber, Torsten; Sauer, Joachim

    2009-01-21

    The methylation of ethene, propene, and t-2-butene by methanol over the acidic microporous H-ZSM-5 catalyst has been investigated by a range of computational methods. Density functional theory (DFT) with periodic boundary conditions (PBE functional) fails to describe the experimentally determined decrease of apparent energy barriers with the alkene size due to inadequate description of dispersion forces. Adding a damped dispersion term expressed as a parametrized sum over atom pair C(6) contributions leads to uniformly underestimated barriers due to self-interaction errors. A hybrid MP2:DFT scheme is presented that combines MP2 energy calculations on a series of cluster models of increasing size with periodic DFT calculations, which allows extrapolation to the periodic MP2 limit. Additionally, errors caused by the use of finite basis sets, contributions of higher order correlation effects, zero-point vibrational energy, and thermal contributions to the enthalpy were evaluated and added to the "periodic" MP2 estimate. This multistep approach leads to enthalpy barriers at 623 K of 104, 77, and 48 kJ/mol for ethene, propene, and t-2-butene, respectively, which deviate from the experimentally measured values by 0, +13, and +8 kJ/mol. Hence, enthalpy barriers can be calculated with near chemical accuracy, which constitutes significant progress in the quantum chemical modeling of reactions in heterogeneous catalysis in general and microporous zeolites in particular.

  11. Discovery of a general method of solving the Schrödinger and dirac equations that opens a way to accurately predictive quantum chemistry.

    PubMed

    Nakatsuji, Hiroshi

    2012-09-18

    Just as Newtonian law governs classical physics, the Schrödinger equation (SE) and the relativistic Dirac equation (DE) rule the world of chemistry. So, if we can solve these equations accurately, we can use computation to predict chemistry precisely. However, for approximately 80 years after the discovery of these equations, chemists believed that they could not solve SE and DE for atoms and molecules that included many electrons. This Account reviews ideas developed over the past decade to further the goal of predictive quantum chemistry. Between 2000 and 2005, I discovered a general method of solving the SE and DE accurately. As a first inspiration, I formulated the structure of the exact wave function of the SE in a compact mathematical form. The explicit inclusion of the exact wave function's structure within the variational space allows for the calculation of the exact wave function as a solution of the variational method. Although this process sounds almost impossible, it is indeed possible, and I have published several formulations and applied them to solve the full configuration interaction (CI) with a very small number of variables. However, when I examined analytical solutions for atoms and molecules, the Hamiltonian integrals in their secular equations diverged. This singularity problem occurred in all atoms and molecules because it originates from the singularity of the Coulomb potential in their Hamiltonians. To overcome this problem, I first introduced the inverse SE and then the scaled SE. The latter simpler idea led to immediate and surprisingly accurate solution for the SEs of the hydrogen atom, helium atom, and hydrogen molecule. The free complement (FC) method, also called the free iterative CI (free ICI) method, was efficient for solving the SEs. In the FC method, the basis functions that span the exact wave function are produced by the Hamiltonian of the system and the zeroth-order wave function. These basis functions are called complement

  12. Quantum chemical studies of trace gas adsorption on ice nanoparticles

    NASA Astrophysics Data System (ADS)

    Schrems, Otto; Ignatov, Stanislav K.; Gadzhiev, Oleg B.; Masunov, Artem E.

    2013-04-01

    We have investigated the interaction of atmospheric trace gases with crystalline water ice particles of nanoscale size by modern quantum chemical methods. Small ice particles which can be formed in different altitudes play an important role in chemistry and physics of the Earth atmosphere. Knowledge about the uptake and incorporation of atmospheric trace gases in ice particles as well as their interactions with water molecules is very important for the understanding of processes at the air/ice interface. The interaction of the atmospheric trace gases with atmospheric ice nanoparticles is also an important issue for the development of modern physicochemical models. Usually, the interactions between trace gases and small particles considered theoretically apply small-size model complexes or the surface models representing only fragments of the ideal surface. Ice particles consisting of 48, 72, 216 and 270 water molecules with a distorted structure of hexagonal water ice Ih were studied using the new SCC-DFTBA method combining well the advantages of the DFT theory and semiempirical methods of quantum chemistry. The largest clusters correspond to the minimal nanoparticle size which are considered to be crystalline as determined experimentally. The clusters up to (H2O)72 were studied at the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(2d,2p) levels. The larger clusters were studied using DFTBA and DFTB+ methods. Several adsorption complexes for the (H2O)270 water ice cluster were optimized at the RI-BLYP/6-31+G(d) theory level to verify the DFTB+ results. Trace gas molecules were coordinated on different sites of the nanoparticles corresponding to different ice Ih crystal planes: (0001), (10-10), (11-20). As atmospheric trace gases we have chosen CO, CO2, HCO*, HCOH*, HCHO, HCOOH and (HCO)2. which are the possible products and intermediates of the UV photolysis of organic molecules such as HCHCHO adsorbed on the ice surface. The structures of the corresponding coordination

  13. Communication: Ro-vibrational control of chemical reactivity in H+CH₄→ H₂+CH₃: full-dimensional quantum dynamics calculations and a sudden model.

    PubMed

    Welsch, Ralph; Manthe, Uwe

    2014-08-01

    The mode-selective chemistry of the title reaction is studied by full-dimensional quantum dynamics simulation on an accurate ab initio potential energy surface for vanishing total angular momentum. Using a rigorous transition state based approach and multi-configurational time-dependent Hartree wave packet propagation, initial state-selected reaction probabilities for many ro-vibrational states of methane are calculated. The theoretical results are compared with experimental trends seen in reactions of methane. An intuitive interpretation of the ro-vibrational control of the chemical reactivity provided by a sudden model based on the quantum transition state concept is discussed.

  14. A combined deuterium NMR and quantum chemical investigation of inequivalent hydrogen bonds in organic solids.

    PubMed

    Webber, Renee; Penner, Glenn H

    2012-01-01

    Deuterium magic angle spinning (MAS) NMR spectroscopy and quantum chemical calculations are used to investigate organic solids in which inequivalent hydrogen bonds are present. The use of (2)H MAS allows one to measure the chemical shift, δ, quadrupolar coupling constant, C(Q), and asymmetry in the quadrupolar interaction, η(Q), for each type of hydrogen bond present in the system. Quantum chemical calculations of the magnetic shielding (σ, which can be related to δ) and the electric field gradient (EFG, which can be related to C(Q)) are compared to the experimental results and are discussed with respect to the relative strengths of the hydrogen bonds within each system.

  15. Electronic and rovibrational quantum chemical analysis of C3P-: the next interstellar anion?

    NASA Astrophysics Data System (ADS)

    Fortenberry, Ryan C.; Lukemire, Joseph A.

    2015-11-01

    C3P- is analogous to the known interstellar anion C3N- with phosphorus replacing nitrogen in a simple step down the periodic table. In this work, it is shown that C3P- is likely to possess a dipole-bound excited state. It has been hypothesized and observationally supported that dipole-bound excited states are an avenue through which anions could be formed in the interstellar medium. Additionally, C3P- has a valence excited state that may lead to further stabilization of this molecule, and C3P- has a larger dipole moment than neutral C3P (˜6 D versus ˜4 D). As such, C3P- is probably a more detectable astromolecule than even its corresponding neutral radical. Highly accurate quantum chemical quartic force fields are also applied to C3P- and its singly 13C substituted isotopologues in order to provide structures, vibrational frequencies, and spectroscopic constants that may aid in its detection.

  16. Conformations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane: are ab initio quantum chemistry predictions accurate?

    NASA Astrophysics Data System (ADS)

    Smith, Grant D.; Jaffe, Richard L.; Yoon, Do. Y.

    1998-06-01

    High-level ab initio quantum chemistry calculations are shown to predict conformer populations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane that are consistent with gas-phase NMR vicinal coupling constant measurements. The conformational energies of the cyclic ether 5-methoxy-1,3-dioxane are found to be consistent with those predicted by a rotational isomeric state (RIS) model based upon the acyclic analog 1,2-dimethoxypropane. The quantum chemistry and RIS calculations indicate the presence of strong attractive 1,5 C(H 3)⋯O electrostatic interactions in these molecules, similar to those found in 1,2-dimethoxyethane.

  17. Quantum mechanical molecular dynamics studies of chemical systems

    NASA Astrophysics Data System (ADS)

    Pavese, Marc

    Methods for including quantum mechanical effects in molecular dynamics (MD) simulations are discussed in this thesis. The thesis focuses on the path integral centroid molecular dynamics (CMD) algorithm. This algorithm is first described and then used in simulations of low temperature para-hydrogen, and also in simulations of the excess proton in water clusters and in the bulk. The CMD method allows one to include the effects of nuclear quantization approximately while still maintaining a quasi-classical, trajectory based, description of the dynamics. The effects of quantization of the electronic degrees of freedom are also discussed. These effects are usually taken into account implicitly through parameterized potential functions. However, methods for including the quantum electronic degrees of freedom explicitly in a MD simulation are also discussed in this thesis. Most notably, the Car-Parrinello method, which combines density functional theory (DFT) with MD, is employed with the CMD algorithm. This yields a method which takes explicit account of the quantum electrons and nuclei. Thus, this work represents one feasible approach for considering the quantum nature of all the degrees of freedom of the system while still maintaining an MD framework. In the concluding remarks, future directions and possibilities for this type of approach are discussed.

  18. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods.

    PubMed

    Kapil, V; VandeVondele, J; Ceriotti, M

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  19. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    NASA Astrophysics Data System (ADS)

    Kapil, V.; VandeVondele, J.; Ceriotti, M.

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  20. Wet chemical synthesis of quantum dots for medical applications

    NASA Astrophysics Data System (ADS)

    Cepeda-Pérez, E. I.; López-Luke, T.; Pérez-Mayen, L.; Hidalgo, Alberto; de la Rosa, E.; Torres-Castro, Alejandro; Ceja-Fdez, Andrea; Vivero-Escoto, Juan; Gonzalez-Yebra, Ana L.

    2015-07-01

    In recent years the use of nanoparticles in medical applications has boomed. This is because the various applications that provide these materials like drug delivery, cancer cell diagnostics and therapeutics [1-5]. Biomedical applications of Quantum Dots (QDs) are focused on molecular imaging and biological sensing due to its optical properties. The size of QDs can be continuously tuned from 2 to 10 nm in diameter, which, after polymer encapsulation, generally increases to 5 - 20 nm diminishing the toxicity. The QDs prepared in our lab have a diameter between 2 to 7 nm. Particles smaller than 5 nm can interact with the cells [2]. Some of the characteristics that distinguish QDs from the commonly used fluorophores are wider range of emission, narrow and more sharply defined emission peak, brighter emission and a higher signal to noise ratio compared with organic dyes [6]. In this paper we will show our progress in the study of the interaction of quantum dots in live cells for image and Raman spectroscopy applications. We will also show the results of the interaction of quantum dots with genomic DNA for diagnostic purposes.

  1. Simulation of chemical reactions in solution by a combination of classical and quantum mechanical approach

    NASA Astrophysics Data System (ADS)

    Onida, Giovanni; Andreoni, Wanda

    1995-09-01

    A classical trajectory mapping method was developed to study chemical reactions in solution and in enzymes. In this method, the trajectories were calculated on a classical potential surface and the free energy profile was obtained by mapping the classical surface to the quantum mechanical surface obtained by the semiempirical AM1 method. There is no need to perform expensive quantum mechanical calculations at each iteration step. This method was applied to proton transfer reactions both in aqueous solution and in papain. The results are encouraging, indicating the applicability of this hybrid method to chemical reactions both in solution and in enzymes.

  2. Predicting drug metabolism by CYP1A1, CYP1A2, and CYP1B1: insights from MetaSite, molecular docking and quantum chemical calculations.

    PubMed

    Pragyan, Preeti; Kesharwani, Siddharth S; Nandekar, Prajwal P; Rathod, Vijay; Sangamwar, Abhay T

    2014-11-01

    Recently, CYP1 enzymes are documented for selective metabolism of anticancer leads in cancer prevention and/or progression. Elucidation of specificity of substrates/inhibitors of CYP1 isoforms plays a vital role in design of more selective and potent anticancer leads. However, an area of concern is the broad range of substrate specificities and planar nature of substrates with limited dataset which makes it difficult to predict their site of metabolism (SOM) accurately. In the present study, various models for prediction of site of metabolism in case of CYP1A1, CYP1A2, and CYP1B1 substrates were developed using MetaSite, molecular docking, and quantum chemical descriptors. The predictive accuracy of MetaSite, molecular docking, and quantum chemical descriptors in identifying experimental site of metabolism was analyzed at three levels; top rank, top three ranks, and top five ranks. Two quantum chemical descriptors, chemical hardness and local nucleophilicity are proposed for the prediction of CYP-mediated SOM for the first time. The predictive accuracy shown by chemical hardness at top three ranks was 83.3, 85.7, and 84.6 % for CYP1A1, CYP1A2 and CYP1B1, respectively, whereas local nucleophilicity gave poor predictions of 50, 42.8, and 46.2 %, respectively. The predictability of chemical hardness descriptor outperformed at all three levels of ranks for CYP1A1, CYP1A2, and CYP1B1. Hence, we propose chemical hardness as an useful quantum chemical descriptor for prediction of metabolically vulnerable prints in CYP1A1, CYP1A2, and CYP1B1 mediated metabolism and support the optimization efforts in drug discovery and development programs.

  3. CHEMICAL SHIFTS IN AMINO ACIDS, PEPTIDES, AND PROTEINS: From Quantum Chemistry to Drug Design

    NASA Astrophysics Data System (ADS)

    Oldfield, Eric

    2002-10-01

    This chapter discusses recent progress in the investigation and use of 13C, 15N, and 19F nuclear magnetic resonance (NMR) chemical shifts and chemical shift tensors in proteins and model systems primarily using quantum chemical (ab initio Hartree-Fock and density functional theory) techniques. Correlations between spectra and structure are made and the techniques applied to other spectroscopic and electrostatic properties as well, including hydrogen bonding, ligand binding to heme proteins, J-couplings, electric field gradients, and atoms-in-molecules theory, together with a brief review of the use of NMR chemical shifts in drug design.

  4. Quantum chemical studies of growth mechanisms of ultrananocrystalline diamond.

    SciTech Connect

    Curtiss, L. A.; Zapol, P.; Sternberg, M.; Redfern, P. C.; Horner, D. A.; Gruen, D. M.; Materials Science Division; North Central Coll.

    2004-06-07

    Computational studies of growth mechanisms on diamond surfaces based on C{sub 2} precursor have been reviewed. The investigations have postulated reaction mechanisms with diamond growth occurring by insertion of C{sub 2} into the C-H bonds of the hydrogen-terminated diamond surface or into {pi}-bonded carbon dimers on dehydrogenated diamond surfaces. Reaction barriers for both growth and renucleation at (011) and (100) diamond surfaces had been calculated using quantum chemistry approaches. Preliminary results on growth mechanism involving CN precursors are also reported.

  5. Studies on the Conformational Landscape of Tert-Butyl Acetate Using Microwave Spectroscopy and Quantum Chemical Calculations

    NASA Astrophysics Data System (ADS)

    Zhao, YueYue; Mouhib, Halima; Li, Guohua; Stahl, Wolfgang; Kleiner, Isabelle

    2014-06-01

    The tert-Butyl acetate molecule was studied using a combination of quantum chemical calculations and molecular beam Fourier transform microwave spectroscopy in the 9 to 14 GHz range. Due to its rather rigid frame, the molecule possesses only two different conformers: one of Cs and one of C1 symmetry. According to ab initio calculations, the Cs conformer is 46 kJ/mol lower in energy and is the one observed in the supersonic jet. We report on the structure and dynamics of the most abundant conformer of tert-butyl acetate, with accurate rotational and centrifugal distortion constants. Additionally, the barrier to internal rotation of the acetyl methyl group was determined. Splittings due to the internal rotation of the methyl group of up to 1.3 GHz were observed in the spectrum. Using the programs XIAM and BELGI-Cs, we determine the barrier height to be about 113 cm-1 and compare the molecular parameters obtained from these two codes. Additionally, the experimental rotational constants were used to validate numerous quantum chemical calculations. This study is part of a larger project which aims at determining the lowest energy conformers of organic esters and ketones which are of interest for flavor or perfume synthetic applications Project partly supported by the PHC PROCOPE 25059YB.

  6. An introduction to quantum chemical methods applied to drug design.

    PubMed

    Stenta, Marco; Dal Peraro, Matteo

    2011-06-01

    The advent of molecular medicine allowed identifying the malfunctioning of subcellular processes as the source of many diseases. Since then, drugs are not only discovered, but actually designed to fulfill a precise task. Modern computational techniques, based on molecular modeling, play a relevant role both in target identification and drug lead development. By flanking and integrating standard experimental techniques, modeling has proven itself as a powerful tool across the drug design process. The success of computational methods depends on a balance between cost (computation time) and accuracy. Thus, the integration of innovative theories and more powerful hardware architectures allows molecular modeling to be used as a reliable tool for rationalizing the results of experiments and accelerating the development of new drug design strategies. We present an overview of the most common quantum chemistry computational approaches, providing for each one a general theoretical introduction to highlight limitations and strong points. We then discuss recent developments in software and hardware resources, which have allowed state-of-the-art of computational quantum chemistry to be applied to drug development.

  7. Experimental and quantum-chemical studies of the reactions of 6-methyluracil with succinic and fumaric acids

    NASA Astrophysics Data System (ADS)

    Terent'ev, A. O.; Borisova, N. S.; Khamitov, E. M.; Zimin, Yu. S.; Mustafin, A. G.

    2014-12-01

    Possible structures of 6-methyluracil complexes with succinic and fumaric acids are studied by quantum-chemical means. The possibility of complex formation occurring between 6-methyluracil and the acids in the ionized and nonionized states is evaluated. The form of the complexes containing the nonionized acid is found to dominate. The quantum-chemical calculation data are consistent with the experimental results.

  8. An efficient matrix product operator representation of the quantum chemical Hamiltonian.

    PubMed

    Keller, Sebastian; Dolfi, Michele; Troyer, Matthias; Reiher, Markus

    2015-12-28

    We describe how to efficiently construct the quantum chemical Hamiltonian operator in matrix product form. We present its implementation as a density matrix renormalization group (DMRG) algorithm for quantum chemical applications. Existing implementations of DMRG for quantum chemistry are based on the traditional formulation of the method, which was developed from the point of view of Hilbert space decimation and attained higher performance compared to straightforward implementations of matrix product based DMRG. The latter variationally optimizes a class of ansatz states known as matrix product states, where operators are correspondingly represented as matrix product operators (MPOs). The MPO construction scheme presented here eliminates the previous performance disadvantages while retaining the additional flexibility provided by a matrix product approach, for example, the specification of expectation values becomes an input parameter. In this way, MPOs for different symmetries - abelian and non-abelian - and different relativistic and non-relativistic models may be solved by an otherwise unmodified program.

  9. Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

    PubMed

    Dreuw, Andreas

    2006-11-13

    With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

  10. An efficient matrix product operator representation of the quantum chemical Hamiltonian

    SciTech Connect

    Keller, Sebastian Reiher, Markus; Dolfi, Michele Troyer, Matthias

    2015-12-28

    We describe how to efficiently construct the quantum chemical Hamiltonian operator in matrix product form. We present its implementation as a density matrix renormalization group (DMRG) algorithm for quantum chemical applications. Existing implementations of DMRG for quantum chemistry are based on the traditional formulation of the method, which was developed from the point of view of Hilbert space decimation and attained higher performance compared to straightforward implementations of matrix product based DMRG. The latter variationally optimizes a class of ansatz states known as matrix product states, where operators are correspondingly represented as matrix product operators (MPOs). The MPO construction scheme presented here eliminates the previous performance disadvantages while retaining the additional flexibility provided by a matrix product approach, for example, the specification of expectation values becomes an input parameter. In this way, MPOs for different symmetries — abelian and non-abelian — and different relativistic and non-relativistic models may be solved by an otherwise unmodified program.

  11. Error Sensitivity to Environmental Noise in Quantum Circuits for Chemical State Preparation.

    PubMed

    Sawaya, Nicolas P D; Smelyanskiy, Mikhail; McClean, Jarrod R; Aspuru-Guzik, Alán

    2016-07-12

    Calculating molecular energies is likely to be one of the first useful applications to achieve quantum supremacy, performing faster on a quantum than a classical computer. However, if future quantum devices are to produce accurate calculations, errors due to environmental noise and algorithmic approximations need to be characterized and reduced. In this study, we use the high performance qHiPSTER software to investigate the effects of environmental noise on the preparation of quantum chemistry states. We simulated 18 16-qubit quantum circuits under environmental noise, each corresponding to a unitary coupled cluster state preparation of a different molecule or molecular configuration. Additionally, we analyze the nature of simple gate errors in noise-free circuits of up to 40 qubits. We find that, in most cases, the Jordan-Wigner (JW) encoding produces smaller errors under a noisy environment as compared to the Bravyi-Kitaev (BK) encoding. For the JW encoding, pure dephasing noise is shown to produce substantially smaller errors than pure relaxation noise of the same magnitude. We report error trends in both molecular energy and electron particle number within a unitary coupled cluster state preparation scheme, against changes in nuclear charge, bond length, number of electrons, noise types, and noise magnitude. These trends may prove to be useful in making algorithmic and hardware-related choices for quantum simulation of molecular energies. PMID:27254482

  12. TOXICOGENOMIC STUDY OF TRIAZOLE FUNGICIDES AND PERFLUOROALKYL ACIDS IN RAT LIVERS ACCURATELY CATEGORIZES CHEMICALS AND IDENTIFIES MECHANISMS OF TOXICITY

    EPA Science Inventory

    Toxicogenomic analysis of five environmental chemicals was performed to investigate the ability of genomics to predict toxicity, categorize chemicals, and elucidate mechanisms of toxicity. Three triazole antifungals (myclobutanil, propiconazole, and triadimefon) and two perfluori...

  13. Recent Results in Quantum Chemical Kinetics from High Resolution Spectroscopy

    SciTech Connect

    Quack, Martin

    2007-12-26

    We outline the approach of our group to derive intramolecular kinetic primary processes from high resolution spectroscopy. We then review recent results on intramolecular vibrational redistribution (IVR) and on tunneling processes. Examples are the quantum dynamics of the C-H-chromophore in organic molecules, hydrogen bond dynamics in (HF){sub 2} and stereomutation dynamics in H{sub 2}O{sub 2} and related chiral molecules. We finally discuss the time scales for these and further processes which range from 10 fs to more than seconds in terms of successive symmetry breakings, leading to the question of nuclear spin symmetry and parity violation as well as the question of CPT symmetry.

  14. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.

    PubMed

    Friesner, Richard A; Guallar, Victor

    2005-01-01

    We describe large scale ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First, technical aspects of the methodology are reviewed, including the hybrid density functional theory (DFT) methods that are typically employed for the QM aspect of the calculations, and various approaches to defining the interface between the QM and MM regions in QM/MM approaches. The modeling of the enzymatic catalytic cycle for three examples--methane monooxygenase, cytochrome P450, and triose phosphate isomerase--are discussed in some depth, followed by a brief summary of other systems that have been investigated by ab initio methods over the past several years. Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects.

  15. Toward Accurate Reaction Energetics for Molecular Line Growth at Surface: Quantum Monte Carlo and Density Functional Theory Calculations

    SciTech Connect

    Kanai, Y; Takeuchi, N

    2009-10-14

    We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.

  16. The Molecular Structure of Phenetole Studied by Microwave Spectroscopy and Quantum Chemical Calculations

    NASA Astrophysics Data System (ADS)

    Ferres, Lynn; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

    2016-06-01

    A pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2 - 26.5 GHz was used to measure the spectrum of phenetole (ethyl phenyl ether or ethoxybenzene, C6H5OC2H5). The conformational landscape is completely determined by the orientations of the phenyl ring and the ethyl group. A two-dimensional potential energy surface was calculated at the MP2/6-311++G(d,p) level of theory. Two conformers were found: The trans conformer has a Cs symmetry, and the gauche conformer has the ethyl group tilted out of the phenyl plane by about 70°. Totally 186 rotational transitions were assigned to the more stable planar trans conformer, and fitted using a semi-rigid rotor model to measurement accuracy of 2 kHz. Highly accurate rotational and centrifugal distortion constants were determined. Several method and basis set combinations were applied to check for convergence and to compare with the experimentally deduced molecular parameters. The inertial defect of the observed conformer Δc = (Ic - Ia - Ib) = -6.718 uÅ2 confirms that the heavy atom skeleton is planar with two pairs of hydrogen atoms out of plane. All lines in the spectrum could be assigned to the trans conformer, which confirms that the gauche conformer cannot be observed under our measurement conditions. In agreement with the rather high torsional barrier of the methyl group (V3 = 1168 wn) calculated by quantum chemical methods, all assigned lines appeared sharp and no signs of splittings were observed for the methyl internal rotation.

  17. Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

    PubMed

    Knizia, Gerald

    2013-11-12

    Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (χ), C 1s core-level shifts, resonance substituent parameters (σR), Lewis structures, and oxidation states of transition-metal complexes.

  18. An integrated experimental and quantum-chemical investigation on the vibrational spectra of chlorofluoromethane

    NASA Astrophysics Data System (ADS)

    Charmet, Andrea Pietropolli; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi; Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cappelli, Chiara; Carnimeo, Ivan; Puzzarini, Cristina

    2013-10-01

    The vibrational analysis of the gas-phase infrared spectra of chlorofluoromethane (CH2ClF, HCFC-31) was carried out in the range 200-6200 cm-1. The assignment of the absorption features in terms of fundamental, overtone, combination, and hot bands was performed on the medium-resolution (up to 0.2 cm-1) Fourier transform infrared spectra. From the absorption cross section spectra accurate values of the integrated band intensities were derived and the global warming potential of this compound was estimated, thus obtaining values of 323, 83, and 42 on a 20-, 100-, and 500-year horizon, respectively. The set of spectroscopic parameters here presented provides the basic data to model the atmospheric behavior of this greenhouse gas. In addition, the obtained vibrational properties were used to benchmark the predictions of state-of-the-art quantum-chemical computational strategies. Extrapolated complete basis set limit values for the equilibrium geometry and harmonic force field were obtained at the coupled-cluster singles and doubles level of theory augmented by a perturbative treatment of triple excitations, CCSD(T), in conjunction with a hierarchical series of correlation-consistent basis sets (cc-pVnZ, with n = T, Q, and 5), taking also into account the core-valence correlation effects and the corrections due to diffuse (aug) functions. To obtain the cubic and quartic semi-diagonal force constants, calculations employing second-order Møller-Plesset perturbation (MP2) theory, the double-hybrid density functional B2PLYP as well as CCSD(T) were performed. For all anharmonic force fields the performances of two different perturbative approaches in computing the vibrational energy levels (i.e., the generalized second order vibrational treatment, GVPT2, and the recently proposed hybrid degeneracy corrected model, HDCPT2) were evaluated and the obtained results allowed us to validate the spectroscopic predictions yielded by the HDCPT2 approach. The predictions of the

  19. An integrated experimental and quantum-chemical investigation on the vibrational spectra of chlorofluoromethane.

    PubMed

    Charmet, Andrea Pietropolli; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi; Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cappelli, Chiara; Carnimeo, Ivan; Puzzarini, Cristina

    2013-10-28

    The vibrational analysis of the gas-phase infrared spectra of chlorofluoromethane (CH2ClF, HCFC-31) was carried out in the range 200-6200 cm(-1). The assignment of the absorption features in terms of fundamental, overtone, combination, and hot bands was performed on the medium-resolution (up to 0.2 cm(-1)) Fourier transform infrared spectra. From the absorption cross section spectra accurate values of the integrated band intensities were derived and the global warming potential of this compound was estimated, thus obtaining values of 323, 83, and 42 on a 20-, 100-, and 500-year horizon, respectively. The set of spectroscopic parameters here presented provides the basic data to model the atmospheric behavior of this greenhouse gas. In addition, the obtained vibrational properties were used to benchmark the predictions of state-of-the-art quantum-chemical computational strategies. Extrapolated complete basis set limit values for the equilibrium geometry and harmonic force field were obtained at the coupled-cluster singles and doubles level of theory augmented by a perturbative treatment of triple excitations, CCSD(T), in conjunction with a hierarchical series of correlation-consistent basis sets (cc-pVnZ, with n = T, Q, and 5), taking also into account the core-valence correlation effects and the corrections due to diffuse (aug) functions. To obtain the cubic and quartic semi-diagonal force constants, calculations employing second-order Møller-Plesset perturbation (MP2) theory, the double-hybrid density functional B2PLYP as well as CCSD(T) were performed. For all anharmonic force fields the performances of two different perturbative approaches in computing the vibrational energy levels (i.e., the generalized second order vibrational treatment, GVPT2, and the recently proposed hybrid degeneracy corrected model, HDCPT2) were evaluated and the obtained results allowed us to validate the spectroscopic predictions yielded by the HDCPT2 approach. The predictions of the

  20. An integrated experimental and quantum-chemical investigation on the vibrational spectra of chlorofluoromethane

    PubMed Central

    Charmet, Andrea Pietropolli; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi; Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cappelli, Chiara; Carnimeo, Ivan; Puzzarini, Cristina

    2015-01-01

    The vibrational analysis of the gas-phase infrared spectra of chlorofluoromethane (CH2ClF, HCFC-31) was carried out in the range 200 – 6200 cm−1. The assignment of the absorption features in terms of fundamental, overtone, combination and hot bands was performed on the medium-resolution (up to 0.2 cm−1) Fourier transform infrared (FTIR) spectra. From the absorption cross section spectra accurate values of the integrated band intensities were derived and the Global Warming Potential (GWP) of this compound was estimated, thus obtaining values of 323, 83 and 42 on a 20-, 100- and 500- year horizon, respectively. The set of spectroscopic parameters here presented provides the basic data to model the atmospheric behavior of this greenhouse gas. In addition, the obtained vibrational properties were used to benchmark the predictions of state-of-the-art quantum-chemical computational strategies. Extrapolated complete basis set (CBS) limit values for the equilibrium geometry and harmonic force field were obtained at the coupled-cluster singles and doubles level of theory augmented by a perturbative treatment of triple excitations, CCSD(T), in conjunction with a hierarchical series of correlation-consistent basis sets (cc-pVnZ, with n = T, Q and 5), taking also into account the core-valence (CV) correlation effects and the corrections due to diffuse (aug) functions. To obtain the cubic and quartic semi-diagonal force constants, calculations employing second-order Møller-Plesset perturbation (MP2) theory, the double-hybrid DFT functional (B2PLYP) as well as CCSD(T) were performed. For all anharmonic force fields the performances of two different perturbative approaches in computing the vibrational energy levels (i.e., the generalized second order vibrational treatment, GVPT2, and the recently proposed hybrid degeneracy corrected model, HDCPT2) were evaluated and the obtained results allowed us to validate the spectroscopic predictions yielded by the HDCPT2 approach

  1. Quantum Chemical Calculations Resolved Identification of Methylnitrocatechols in Atmospheric Aerosols.

    PubMed

    Frka, Sanja; Šala, Martin; Kroflič, Ana; Huš, Matej; Čusak, Alen; Grgić, Irena

    2016-06-01

    Methylnitrocatechols (MNCs) are secondary organic aerosol (SOA) tracers and major contributors to atmospheric brown carbon; however, their formation and aging processes in atmospheric waters are unknown. To investigate the importance of aqueous-phase electrophilic substitution of 3-methylcatechol with nitronium ion (NO2(+)), we performed quantum calculations of their favorable pathways. The calculations predicted the formation of 3-methyl-5-nitrocatechol (3M5NC), 3-methyl-4-nitrocatechol (3M4NC), and a negligible amount of 3-methyl-6-nitrocatechol (3M6NC). MNCs in atmospheric PM2 samples were further inspected by LC/(-)ESI-MS/MS using commercial as well as de novo synthesized authentic standards. We detected 3M5NC and, for the first time, 3M4NC. In contrast to previous reports, 3M6NC was not observed. Agreement between calculated and observed 3M5NC/3M4NC ratios cannot unambiguously confirm the electrophilic mechanism as the exclusive formation pathway of MNCs in aerosol water. However, the examined nitration by NO2(+) is supported by (1) the absence of 3M6NC in the ambient aerosols analyzed and (2) the constant 3M5NC/3M4NC ratio in field aerosol samples, which indicates their common formation pathway. The magnitude of error one could make by incorrectly identifying 3M4NC as 3M6NC in ambient aerosols was also assessed, suggesting the importance of evaluating the literature regarding MNCs with special care.

  2. Quantum Chemical Calculations Resolved Identification of Methylnitrocatechols in Atmospheric Aerosols.

    PubMed

    Frka, Sanja; Šala, Martin; Kroflič, Ana; Huš, Matej; Čusak, Alen; Grgić, Irena

    2016-06-01

    Methylnitrocatechols (MNCs) are secondary organic aerosol (SOA) tracers and major contributors to atmospheric brown carbon; however, their formation and aging processes in atmospheric waters are unknown. To investigate the importance of aqueous-phase electrophilic substitution of 3-methylcatechol with nitronium ion (NO2(+)), we performed quantum calculations of their favorable pathways. The calculations predicted the formation of 3-methyl-5-nitrocatechol (3M5NC), 3-methyl-4-nitrocatechol (3M4NC), and a negligible amount of 3-methyl-6-nitrocatechol (3M6NC). MNCs in atmospheric PM2 samples were further inspected by LC/(-)ESI-MS/MS using commercial as well as de novo synthesized authentic standards. We detected 3M5NC and, for the first time, 3M4NC. In contrast to previous reports, 3M6NC was not observed. Agreement between calculated and observed 3M5NC/3M4NC ratios cannot unambiguously confirm the electrophilic mechanism as the exclusive formation pathway of MNCs in aerosol water. However, the examined nitration by NO2(+) is supported by (1) the absence of 3M6NC in the ambient aerosols analyzed and (2) the constant 3M5NC/3M4NC ratio in field aerosol samples, which indicates their common formation pathway. The magnitude of error one could make by incorrectly identifying 3M4NC as 3M6NC in ambient aerosols was also assessed, suggesting the importance of evaluating the literature regarding MNCs with special care. PMID:27136117

  3. Quantum Chemical Simulation of Carbon Nanotube Nucleation on Al2O3 Catalysts via CH4 Chemical Vapor Deposition.

    PubMed

    Page, Alister J; Saha, Supriya; Li, Hai-Bei; Irle, Stephan; Morokuma, Keiji

    2015-07-29

    We present quantum chemical simulations demonstrating how single-walled carbon nanotubes (SWCNTs) form, or "nucleate", on the surface of Al2O3 nanoparticles during chemical vapor deposition (CVD) using CH4. SWCNT nucleation proceeds via the formation of extended polyyne chains that only interact with the catalyst surface at one or both ends. Consequently, SWCNT nucleation is not a surface-mediated process. We demonstrate that this unusual nucleation sequence is due to two factors. First, the π interaction between graphitic carbon and Al2O3 is extremely weak, such that graphitic carbon is expected to desorb at typical CVD temperatures. Second, hydrogen present at the catalyst surface actively passivates dangling carbon bonds, preventing a surface-mediated nucleation mechanism. The simulations reveal hydrogen's reactive chemical pathways during SWCNT nucleation and that the manner in which SWCNTs form on Al2O3 is fundamentally different from that observed using "traditional" transition metal catalysts. PMID:26148208

  4. Chemically Triggered Formation of Two-Dimensional Epitaxial Quantum Dot Superlattices.

    PubMed

    Walravens, Willem; De Roo, Jonathan; Drijvers, Emile; Ten Brinck, Stephanie; Solano, Eduardo; Dendooven, Jolien; Detavernier, Christophe; Infante, Ivan; Hens, Zeger

    2016-07-26

    Two dimensional superlattices of epitaxially connected quantum dots enable size-quantization effects to be combined with high charge carrier mobilities, an essential prerequisite for highly performing QD devices based on charge transport. Here, we demonstrate that surface active additives known to restore nanocrystal stoichiometry can trigger the formation of epitaxial superlattices of PbSe and PbS quantum dots. More specifically, we show that both chalcogen-adding (sodium sulfide) and lead oleate displacing (amines) additives induce small area epitaxial superlattices of PbSe quantum dots. In the latter case, the amine basicity is a sensitive handle to tune the superlattice symmetry, with strong and weak bases yielding pseudohexagonal or quasi-square lattices, respectively. Through density functional theory calculations and in situ titrations monitored by nuclear magnetic resonance spectroscopy, we link this observation to the concomitantly different coordination enthalpy and ligand displacement potency of the amine. Next to that, an initial ∼10% reduction of the initial ligand density prior to monolayer formation and addition of a mild, lead oleate displacing chemical trigger such as aniline proved key to induce square superlattices with long-range, square micrometer order; an effect that is the more pronounced the larger the quantum dots. Because the approach applies to PbS quantum dots as well, we conclude that it offers a reproducible and rational method for the formation of highly ordered epitaxial quantum dot superlattices. PMID:27383262

  5. Chemically Triggered Formation of Two-Dimensional Epitaxial Quantum Dot Superlattices.

    PubMed

    Walravens, Willem; De Roo, Jonathan; Drijvers, Emile; Ten Brinck, Stephanie; Solano, Eduardo; Dendooven, Jolien; Detavernier, Christophe; Infante, Ivan; Hens, Zeger

    2016-07-26

    Two dimensional superlattices of epitaxially connected quantum dots enable size-quantization effects to be combined with high charge carrier mobilities, an essential prerequisite for highly performing QD devices based on charge transport. Here, we demonstrate that surface active additives known to restore nanocrystal stoichiometry can trigger the formation of epitaxial superlattices of PbSe and PbS quantum dots. More specifically, we show that both chalcogen-adding (sodium sulfide) and lead oleate displacing (amines) additives induce small area epitaxial superlattices of PbSe quantum dots. In the latter case, the amine basicity is a sensitive handle to tune the superlattice symmetry, with strong and weak bases yielding pseudohexagonal or quasi-square lattices, respectively. Through density functional theory calculations and in situ titrations monitored by nuclear magnetic resonance spectroscopy, we link this observation to the concomitantly different coordination enthalpy and ligand displacement potency of the amine. Next to that, an initial ∼10% reduction of the initial ligand density prior to monolayer formation and addition of a mild, lead oleate displacing chemical trigger such as aniline proved key to induce square superlattices with long-range, square micrometer order; an effect that is the more pronounced the larger the quantum dots. Because the approach applies to PbS quantum dots as well, we conclude that it offers a reproducible and rational method for the formation of highly ordered epitaxial quantum dot superlattices.

  6. Accurate Ab Initio Quantum Mechanics Simulations of Bi2Se3 and Bi2Te3 Topological Insulator Surfaces.

    PubMed

    Crowley, Jason M; Tahir-Kheli, Jamil; Goddard, William A

    2015-10-01

    It has been established experimentally that Bi2Te3 and Bi2Se3 are topological insulators, with zero band gap surface states exhibiting linear dispersion at the Fermi energy. Standard density functional theory (DFT) methods such as PBE lead to large errors in the band gaps for such strongly correlated systems, while more accurate GW methods are too expensive computationally to apply to the thin films studied experimentally. We show here that the hybrid B3PW91 density functional yields GW-quality results for these systems at a computational cost comparable to PBE. The efficiency of our approach stems from the use of Gaussian basis functions instead of plane waves or augmented plane waves. This remarkable success without empirical corrections of any kind opens the door to computational studies of real chemistry involving the topological surface state, and our approach is expected to be applicable to other semiconductors with strong spin-orbit coupling.

  7. Exploiting Locality in Quantum Computation for Quantum Chemistry.

    PubMed

    McClean, Jarrod R; Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

    2014-12-18

    Accurate prediction of chemical and material properties from first-principles quantum chemistry is a challenging task on traditional computers. Recent developments in quantum computation offer a route toward highly accurate solutions with polynomial cost; however, this solution still carries a large overhead. In this Perspective, we aim to bring together known results about the locality of physical interactions from quantum chemistry with ideas from quantum computation. We show that the utilization of spatial locality combined with the Bravyi-Kitaev transformation offers an improvement in the scaling of known quantum algorithms for quantum chemistry and provides numerical examples to help illustrate this point. We combine these developments to improve the outlook for the future of quantum chemistry on quantum computers.

  8. Accurate relativistic energy-consistent pseudopotentials for the superheavy elements 111 to 118 including quantum electrodynamic effects

    NASA Astrophysics Data System (ADS)

    Hangele, Tim; Dolg, Michael; Hanrath, Michael; Cao, Xiaoyan; Schwerdtfeger, Peter

    2012-06-01

    Energy-consistent two-component semi-local pseudopotentials for the superheavy elements with atomic numbers 111-118 have been adjusted to fully relativistic multi-configuration Dirac-Hartree-Fock calculations based on the Dirac-Coulomb Hamiltonian, including perturbative corrections for the frequency-dependent Breit interaction in the Coulomb gauge and lowest-order quantum electrodynamic effects. The pseudopotential core includes 92 electrons corresponding to the configuration [Xe]4f 145d105f 14. The parameters for the elements 111-118 were fitted by two-component multi-configuration Hartree-Fock calculations in the intermediate coupling scheme to the total energies of 267 up to 797 J levels arising from 31 up to 62 nonrelativistic configurations, including also anionic and highly ionized states, with mean absolute errors clearly below 0.02 eV for averages corresponding to nonrelativistic configurations. Primitive basis sets for one- and two-component pseudopotential calculations have been optimized for the ground and excited states and exhibit finite basis set errors with respect to the finite-difference Hartree-Fock limit below 0.01 and 0.02 eV, respectively. General contraction schemes have been applied to obtain valence basis sets of polarized valence double- to quadruple-zeta quality. Results of atomic test calculations in the intermediate coupling scheme at the Fock-space coupled-cluster level are in good agreement with those of corresponding fully relativistic all-electron calculations based on the Dirac-Coulomb-Breit Hamiltonian. The results demonstrate besides the well-known need of a relativistic treatment at the Dirac-Coulomb level also the necessity to include higher-order corrections for the superheavy elements.

  9. Accurate relativistic energy-consistent pseudopotentials for the superheavy elements 111 to 118 including quantum electrodynamic effects.

    PubMed

    Hangele, Tim; Dolg, Michael; Hanrath, Michael; Cao, Xiaoyan; Schwerdtfeger, Peter

    2012-06-01

    Energy-consistent two-component semi-local pseudopotentials for the superheavy elements with atomic numbers 111-118 have been adjusted to fully relativistic multi-configuration Dirac-Hartree-Fock calculations based on the Dirac-Coulomb Hamiltonian, including perturbative corrections for the frequency-dependent Breit interaction in the Coulomb gauge and lowest-order quantum electrodynamic effects. The pseudopotential core includes 92 electrons corresponding to the configuration [Xe]4f(14)5d(10)5f(14). The parameters for the elements 111-118 were fitted by two-component multi-configuration Hartree-Fock calculations in the intermediate coupling scheme to the total energies of 267 up to 797 J levels arising from 31 up to 62 nonrelativistic configurations, including also anionic and highly ionized states, with mean absolute errors clearly below 0.02 eV for averages corresponding to nonrelativistic configurations. Primitive basis sets for one- and two-component pseudopotential calculations have been optimized for the ground and excited states and exhibit finite basis set errors with respect to the finite-difference Hartree-Fock limit below 0.01 and 0.02 eV, respectively. General contraction schemes have been applied to obtain valence basis sets of polarized valence double- to quadruple-zeta quality. Results of atomic test calculations in the intermediate coupling scheme at the Fock-space coupled-cluster level are in good agreement with those of corresponding fully relativistic all-electron calculations based on the Dirac-Coulomb-Breit Hamiltonian. The results demonstrate besides the well-known need of a relativistic treatment at the Dirac-Coulomb level also the necessity to include higher-order corrections for the superheavy elements. PMID:22697528

  10. Combined spectroscopic and quantum chemical studies of ezetimibe

    NASA Astrophysics Data System (ADS)

    Prajapati, Preeti; Pandey, Jaya; Shimpi, Manishkumar R.; Srivastava, Anubha; Tandon, Poonam; Velaga, Sitaram P.; Sinha, Kirti

    2016-12-01

    Ezetimibe (EZT) is a hypocholesterolemic agent used for the treatment of elevated blood cholesterol levels as it lowers the blood cholesterol by blocking the absorption of cholesterol in intestine. Study aims to combine experimental and computational methods to provide insights into the structural and vibrational spectroscopic properties of EZT which is important for explaining drug substance physical and biological properties. Computational study on molecular properties of ezetimibe is presented using density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set. A detailed vibrational assignment has been done for the observed IR and Raman spectra of EZT. In addition to the conformational study, hydrogen bonding and molecular docking studies have been also performed. For conformational studies, the double well potential energy curves have been plotted for the rotation around the six flexible bonds of the molecule. UV absorption spectrum was examined in methanol solvent and compared with calculated one in solvent environment (IEF-PCM) using TD-DFT/6-31G basis set. HOMO-LUMO energy gap of both the conformers have also been calculated in order to predict its chemical reactivity and stability. The stability of the molecule was also examined by means of natural bond analysis (NBO) analysis. To account for the chemical reactivity and site selectivity of the molecules, molecular electrostatic potential (MEPS) map has been plotted. The combination of experimental and calculated results provide an insight into the structural and vibrational spectroscopic properties of EZT. In order to give an insight for the biological activity of EZT, molecular docking of EZT with protein NPC1L1 has been done.

  11. A DPF Analysis Yields Quantum Mechanically Accurate Analytic Potential Energy Functions for the a ^1Σ^+ and X ^1Σ^+ States of NaH

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Walji, Sadru; Sentjens, Katherine

    2013-06-01

    Alkali hydride diatomic molecules have long been the object of spectroscopic studies. However, their small reduced mass makes them species for which the conventional semiclassical-based methods of analysis tend to have the largest errors. To date, the only quantum-mechanically accurate direct-potential-fit (DPF) analysis for one of these molecules was the one for LiH reported by Coxon and Dickinson. The present paper extends this level of analysis to NaH, and reports a DPF analysis of all available spectroscopic data for the A ^1Σ^+-X ^1Σ^+ system of NaH which yields analytic potential energy functions for these two states that account for those data (on average) to within the experimental uncertainties. W.C. Stwalley, W.T. Zemke and S.C. Yang, J. Phys. Chem. Ref. Data {20}, 153-187 (1991). J.A. Coxon and C.S. Dickinson, J. Chem. Phys. {121}, 8378 (2004).

  12. The nature and role of quantized transition states in the accurate quantum dynamics of the reaction O + H2 yields OH + H

    NASA Technical Reports Server (NTRS)

    Chatfield, David C.; Friedman, Ronald S.; Lynch, Gillian C.; Truhlar, Donald G.; Schwenke, David W.

    1993-01-01

    Accurate quantum mechanical dynamics calculations are reported for the reaction probabilities of O(3P) + H2 yields OH + H with zero total angular momentum on a single potential energy surface. The results show that the reactive flux is gated by quantized transition states up to the highest energy studied, which corresponds to a total energy of 1.90 eV. The quantized transition states are assigned and compared to vibrationally adiabatic barrier maxima; their widths and transmission coefficients are determined; and they are classified as variational, supernumerary of the first kind, and supernumerary of the second kind. Their effects on state-selected and state-to-state reactivity are discussed in detail.

  13. Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence.

    PubMed

    de la Lande, Aurélien; Řezáč, Jan; Lévy, Bernard; Sanders, Barry C; Salahub, Dennis R

    2011-03-23

    Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.

  14. Quantum Isostere Database: a web-based tool using quantum chemical topology to predict bioisosteric replacements for drug design.

    PubMed

    Devereux, Mike; Popelier, Paul L A; McLay, Iain M

    2009-06-01

    This paper introduces the 'Quantum Isostere Database' (QID), a Web-based tool designed to find bioisosteric fragment replacements for lead optimization using stored ab initio data. A wide range of original geometric, electronic, and calculated physical properties are stored for each fragment. Physical descriptors with clear meaning are chosen, such as distribution of electrostatic potential energy values across a fragment surface and geometric parameters to describe fragment conformation and shape from ab initio structures. Further fundamental physical properties are linked to broader chemical characteristics relevant to biological activity, such as H-bond donor and acceptor strengths. Additional properties with less easily interpretable links to biological activity are also stored to allow future development of QSAR/QSPR models for quantities such as pK(a) and solubility. Conformational dependence of the ab initio descriptors is explicitly dealt with by storing properties for a variety of low-energy conformers of each fragment. Capping groups are used in ab initio calculations to represent different chemical environments, based on background research into transferability of electronic descriptors [J. Comput. Chem. 2009, 30, 1300-1318]. The resulting database has a Web interface that allows medicinal chemists to enter a query fragment, select important chemical features, and retrieve a list of suggested replacements with similar chemical characteristics. Examples of known bioisosteric replacements correctly identified by the QID tool are given.

  15. Spectroscopic analysis of cinnamic acid using quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Vinod, K. S.; Periandy, S.; Govindarajan, M.

    2015-02-01

    In this present study, FT-IR, FT-Raman, 13C NMR and 1H NMR spectra for cinnamic acid have been recorded for the vibrational and spectroscopic analysis. The observed fundamental frequencies (IR and Raman) were assigned according to their distinctiveness region. The computed frequencies and optimized parameters have been calculated by using HF and DFT (B3LYP) methods and the corresponding results are tabulated. On the basis of the comparison between computed and experimental results assignments of the fundamental vibrational modes are examined. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The alternation of the vibration pattern of the pedestal molecule related to the substitutions was analyzed. The 13C and 1H NMR spectra have been recorded and the chemical shifts have been calculated using the gauge independent atomic orbital (GIAO) method. The Mulliken charges, UV spectral analysis and HOMO-LUMO analysis of have been calculated and reported. The molecular electrostatic potential (MEP) was constructed.

  16. Spectroscopic analysis of cinnamic acid using quantum chemical calculations.

    PubMed

    Vinod, K S; Periandy, S; Govindarajan, M

    2015-02-01

    In this present study, FT-IR, FT-Raman, (13)C NMR and (1)H NMR spectra for cinnamic acid have been recorded for the vibrational and spectroscopic analysis. The observed fundamental frequencies (IR and Raman) were assigned according to their distinctiveness region. The computed frequencies and optimized parameters have been calculated by using HF and DFT (B3LYP) methods and the corresponding results are tabulated. On the basis of the comparison between computed and experimental results assignments of the fundamental vibrational modes are examined. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The alternation of the vibration pattern of the pedestal molecule related to the substitutions was analyzed. The (13)C and (1)H NMR spectra have been recorded and the chemical shifts have been calculated using the gauge independent atomic orbital (GIAO) method. The Mulliken charges, UV spectral analysis and HOMO-LUMO analysis of have been calculated and reported. The molecular electrostatic potential (MEP) was constructed.

  17. Chemical Exchange Saturation Transfer (CEST) Agents: Quantum Chemistry and MRI.

    PubMed

    Li, Jikun; Feng, Xinxin; Zhu, Wei; Oskolkov, Nikita; Zhou, Tianhui; Kim, Boo Kyung; Baig, Noman; McMahon, Michael T; Oldfield, Eric

    2016-01-01

    Diamagnetic chemical exchange saturation transfer (CEST) contrast agents offer an alternative to Gd(3+) -based contrast agents for MRI. They are characterized by containing protons that can rapidly exchange with water and it is advantageous to have these protons resonate in a spectral window that is far removed from water. Herein, we report the first results of DFT calculations of the (1) H nuclear magnetic shieldings in 41 CEST agents, finding that the experimental shifts can be well predicted (R(2) =0.882). We tested a subset of compounds with the best MRI properties for toxicity and for activity as uncouplers, then obtained mice kidney CEST MRI images for three of the most promising leads finding 16 (2,4-dihydroxybenzoic acid) to be one of the most promising CEST MRI contrast agents to date. Overall, the results are of interest since they show that (1) H NMR shifts for CEST agents-charged species-can be well predicted, and that several leads have low toxicity and yield good in vivo MR images.

  18. Catalytic performance of carbon nanotubes in H2O2 decomposition: experimental and quantum chemical study.

    PubMed

    Voitko, Katerina; Tóth, Ajna; Demianenko, Evgenij; Dobos, Gábor; Berke, Barbara; Bakalinska, Olga; Grebenyuk, Anatolij; Tombácz, Etelka; Kuts, Volodymyr; Tarasenko, Yurij; Kartel, Mykola; László, Krisztina

    2015-01-01

    The catalytic performance of multi-walled carbon nanotubes (MWCNTs) with different surface chemistry was studied in the decomposition reaction of H2O2 at various values of pH and temperature. A comparative analysis of experimental and quantum chemical calculation results is given. It has been shown that both the lowest calculated activation energy (∼18.9 kJ/mol) and the highest rate constant correspond to the N-containing CNT. The calculated chemisorption energy values correlate with the operation stability of MWCNTs. Based on the proposed quantum chemical model it was found that the catalytic activity of carbon materials in electron transfer reactions is controlled by their electron donor capability.

  19. Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action

    PubMed Central

    Gusenleitner, Daniel; Auerbach, Scott S.; Melia, Tisha; Gómez, Harold F.; Sherr, David H.; Monti, Stefano

    2014-01-01

    Background Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, fewer than 2% of the chemicals on the market have actually been tested. However, evidence accumulated to date suggests that gene expression profiles from model organisms exposed to chemical compounds reflect underlying mechanisms of action, and that these toxicogenomic models could be used in the prediction of chemical carcinogenicity. Results In this study, we used a rat-based microarray dataset from the NTP DrugMatrix Database to test the ability of toxicogenomics to model carcinogenicity. We analyzed 1,221 gene-expression profiles obtained from rats treated with 127 well-characterized compounds, including genotoxic and non-genotoxic carcinogens. We built a classifier that predicts a chemical's carcinogenic potential with an AUC of 0.78, and validated it on an independent dataset from the Japanese Toxicogenomics Project consisting of 2,065 profiles from 72 compounds. Finally, we identified differentially expressed genes associated with chemical carcinogenesis, and developed novel data-driven approaches for the molecular characterization of the response to chemical stressors. Conclusion Here, we validate a toxicogenomic approach to predict carcinogenicity and provide strong evidence that, with a larger set of compounds, we should be able to improve the sensitivity and specificity of the predictions. We found that the prediction of carcinogenicity is tissue-dependent and that the results also confirm and expand upon previous studies implicating DNA damage, the peroxisome proliferator-activated receptor, the aryl hydrocarbon receptor, and regenerative pathology in the response to carcinogen exposure. PMID:25058030

  20. Determination of atropisomeric configurations of macrocyclic bisbibenzyls by HPLC-CD/UV and quantum chemical calculations.

    PubMed

    Wang, Li-Ning; Xie, Chun-Feng; Zhu, Xiao-Song; Fan, Pei-Hong; Lou, Hong-Xiang

    2011-04-01

    Isoriccardin C (1) and riccardin D (2), isolated from the liverwort Reboulia hemisphaerica, were first characterized to be a mixture of two enantiomeric atropisomers by online chiral high-performance liquid chromatography-circular dichroism (HPLC-CD) analysis. Exemplarily for bisbibenzyls of the diarylether-biphenyl type, the absolute atropisomeric configurations of compunds 1 and 2 were determined by the analysis of their CD data coupled with quantum chemical CD calculations.

  1. Kirkwood-Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies.

    PubMed

    Chiba, Shuntaro; Furuta, Tadaomi; Shimizu, Seishi

    2016-08-11

    Cosolvents, such as urea, affect protein folding and binding, and the solubility of solutes. The modeling of cosolvents has been facilitated significantly by the rigorous Kirkwood-Buff (KB) theory of solutions, which can describe structural thermodynamics over the entire composition range of aqueous cosolvent mixtures based only on the solution density and the KB integrals (KBIs), i.e., the net excess radial distribution functions from the bulk. Using KBIs to describe solution thermodynamics has given rise to a clear guideline that an accurate prediction of KBIs is equivalent to accurate modeling of cosolvents. Taking urea as an example, here we demonstrate that an improvement in the prediction of KBIs comes from an improved reproduction of high-level quantum chemical (QC) electrostatic potential and molecular pairwise interaction energies. This rational approach to the improvement of the KBI prediction stems from a comparison of existing force fields, AMOEBA, and the generalized AMBER force field, as well as the further optimization of the former to enable better agreement with QC interaction energies. Such improvements would pave the way toward a rational and systematic determination of the transferable force field parameters for a number of important small molecule cosolvents. PMID:27434200

  2. Sub-nanometrically resolved chemical mappings of quantum-cascade laser active regions

    NASA Astrophysics Data System (ADS)

    Pantzas, Konstantinos; Beaudoin, Grégoire; Patriarche, Gilles; Largeau, Ludovic; Mauguin, Olivia; Pegolotti, Giulia; Vasanelli, Angela; Calvar, Ariane; Amanti, Maria; Sirtori, Carlo; Sagnes, Isabelle

    2016-05-01

    A procedure that produces sub-nanometrically resolved chemical mappings of MOCVD-grown InGaAs/InAlAs/InP quantum cascade lasers is presented. The chemical mappings reveal that, although the structure is lattice-matched to InP, the InAlAs barriers do not attain the nominal aluminum content—48%—and are, in fact, InGaAlAs quaternaries. This information is used to adjust the aluminum precursor flow and fine-tune the composition of the barriers, resulting in a significant improvement of the fabricated lasers.

  3. Monocrystalline molybdenum silicide based quantum dot superlattices grown by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Savelli, Guillaume; Silveira Stein, Sergio; Bernard-Granger, Guillaume; Faucherand, Pascal; Montès, Laurent

    2016-09-01

    This paper presents the growth of doped monocrystalline molybdenum-silicide-based quantum dot superlattices (QDSL). This is the first time that such nanostructured materials integrating molybdenum silicide nanodots have been grown. QDSL are grown by reduced pressure chemical vapor deposition (RPCVD). We present here their crystallographic structures and chemical properties, as well as the influence of the nanostructuration on their thermal and electrical properties. Particularly, it will be shown some specific characteristics for these QDSL, such as a localization of nanodots between the layers, unlike other silicide based QDSL, an accumulation of doping atoms near the nanodots, and a strong decrease of the thermal conductivity obtained thanks to the nanostructuration.

  4. Quantum Cascade Laser Development Efforts for Implementation into Chemical and Remote Sensing Systems

    SciTech Connect

    Wojcik, Michael D.; Myers, Tanya L.; Taubman, Matthew S.; Cannon, Bret D.; Broocks, Bryan T.; Mosely, Trinesha

    2004-12-01

    Quantum cascade lasers (QCL) offer many desirable attributes as mid-infrared laser sources for chemical and remote sensing. Some key advantages are a narrow linewidth, wide bandwidth current modulation characteristics and moderate tunability (15 cm-1). Combined, these characteristics allow for applications to a wide variety of chemical and remote sensing techniques such as wavelength and frequency modulation based detection techniques, cavity enhanced point sensors as well as techniques such as LIDAR and DIAL. This paper will describe laser development efforts to enhance QCL frequency stabilization and QCL injection locking and to develop robust external cavity QCL designs.

  5. An Effective Two-Orbital Quantum Chemical Model for Organic Photovoltaic Materials.

    PubMed

    Raos, Guido; Casalegno, Mosè; Idé, Julien

    2014-01-14

    We present a coarse-grained quantum chemical model of organic photovoltaic materials, which is based on the classic idea that the main physical processes involve the electrons occupying the frontier orbitals (HOMO and LUMO) of each molecule or "site". This translates into an effective electronic Hamiltonian with two electrons and two orbitals per site. The on-site parameters (one- and two-electron integrals) can be rigorously related to the ionization energy, electron affinity, and singlet and triplet first excitation energies of that site. The intersite Hamiltonian parameters are introduced in a way that is consistent with classical electrostatics, and for the one-electron part, we use a simple approximation that could be refined using information from atomistic quantum chemical calculations. The model has been implemented within the GAMESS-US package. This allows the exploration of the physics of these materials using state-of-the art quantum chemical methods on relatively large systems (hundreds of electron-donor and electron-acceptor sites). To illustrate this point, we present ground- and excited-state calculations on dimers and two-dimensional arrays of sites using the Hartree-Fock, configuration interaction, and coupled-cluster methods. The calculations provide evidence for the possibility of low-energy, long-range electron transfer in donor-acceptor heterojunctions characterized by a moderate degree of disorder.

  6. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy.

    PubMed

    Zhang, Rongchun; Mroue, Kamal H; Ramamoorthy, Ayyalusamy

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110-120 kHz), (1)H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong (1)H-(1)H homonuclear dipolar couplings and narrow (1)H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) (1)H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about (1)H-(1)H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical

  7. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    SciTech Connect

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic

  8. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

    SciTech Connect

    Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I.; Merz, Kenneth M. Jr; Westerhoff, Lance M.

    2014-05-01

    Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

  9. Chemical modification of Hyflon® AD copolymer end groups by means of physical and chemical treatments. A joint spectroscopic and quantum chemical investigation

    NASA Astrophysics Data System (ADS)

    Radice, Stefano; Canil, Giorgio; Millefanti, Stefano; Tortelli, Vito; Milani, Alberto; Castiglioni, Chiara

    2015-06-01

    In this paper is presented a study on the effects of physical treatments, namely electron beam irradiation or fluorination, on a perfluoropolymer copolymer of tetrafluoroethylene with 2,2,4-trifluoro-5-trifluoromethoxy-1,3-dioxole (Hyflon® AD copolymer). The analysis has been carried out by means of IR spectroscopy and quantum chemical modeling based on density functional theory; this combined experimental/theoretical approach has proven effective for the interpretation of previously unassigned IR bands, which are associated to functional groups generated by polymer degradation and chain scission. We performed a systematic screening of chemical groups and structures compatible with degradation pathways that are possible from the chemical point of view: the chemical mechanisms and the correlation with the spectroscopic experimental data (both frequency and intensity) provide guidelines in understanding the phenomena. Moreover, the spectroscopic experimental/theoretical and chemical approaches allowed us to identify some chemical structures responsible for the unassigned IR bands in the Cdbnd O stretching frequency region above 1800 cm-1, which is typical for carbonyl groups in fluorinated systems.

  10. The Radical Pair Mechanism and the Avian Chemical Compass: Quantum Coherence and Entanglement

    SciTech Connect

    Zhang, Yiteng; Kais, Sabre; Berman, Gennady Petrovich

    2015-02-02

    We review the spin radical pair mechanism which is a promising explanation of avian navigation. This mechanism is based on the dependence of product yields on 1) the hyperfine interaction involving electron spins and neighboring nuclear spins and 2) the intensity and orientation of the geomagnetic field. One surprising result is that even at ambient conditions quantum entanglement of electron spins can play an important role in avian magnetoreception. This review describes the general scheme of chemical reactions involving radical pairs generated from singlet and triplet precursors; the spin dynamics of the radical pairs; and the magnetic field dependence of product yields caused by the radical pair mechanism. The main part of the review includes a description of the chemical compass in birds. We review: the general properties of the avian compass; the basic scheme of the radical pair mechanism; the reaction kinetics in cryptochrome; quantum coherence and entanglement in the avian compass; and the effects of noise. We believe that the quantum avian compass can play an important role in avian navigation and can also provide the foundation for a new generation of sensitive and selective magnetic-sensing nano-devices.

  11. Grid-based methods for biochemical ab initio quantum chemical applications

    SciTech Connect

    Colvin, M.E.; Nelson, J.S.; Mori, E.

    1997-01-01

    A initio quantum chemical methods are seeing increased application in a large variety of real-world problems including biomedical applications ranging from drug design to the understanding of environmental mutagens. The vast majority of these quantum chemical methods are {open_quotes}spectral{close_quotes}, that is they describe the charge distribution around the nuclear framework in terms of a fixed analytic basis set. Despite the additional complexity they bring, methods involving grid representations of the electron or solvent charge can provide more efficient schemes for evaluating spectral operators, inexpensive methods for calculating electron correlation, and methods for treating the electrostatic energy of salvation in polar solvents. The advantage of mixed or {open_quotes}pseudospectral{close_quotes} methods is that they allow individual non-linear operators in the partial differential equations, such as coulomb operators, to be calculated in the most appropriate regime. Moreover, these molecular grids can be used to integrate empirical functionals of the electron density. These so-called density functional methods (DFT) are an extremely promising alternative to conventional post-Hartree Fock quantum chemical methods. The introduction of a grid at the molecular solvent-accessible surface allows a very sophisticated treatment of a polarizable continuum solvent model (PCM). Where most PCM approaches use a truncated expansion of the solute`s electric multipole expansion, e.g. net charge (Born model) or dipole moment (Onsager model), such a grid-based boundary-element method (BEM) yields a nearly exact treatment of the solute`s electric field. This report describes the use of both DFT and BEM methods in several biomedical chemical applications.

  12. Quantum Chemical Studies of Actinides and Lanthanides: From Small Molecules to Nanoclusters

    NASA Astrophysics Data System (ADS)

    Vlaisavljevich, Bess

    Research into actinides is of high interest because of their potential applications as an energy source and for the environmental implications therein. Global concern has arisen since the development of the actinide concept in the 1940s led to the industrial scale use of the commercial nuclear energy cycle and nuclear weapons production. Large quantities of waste have been generated from these processes inspiring efforts to address fundamental questions in actinide science. In this regard, the objective of this work is to use theory to provide insight and predictions into actinide chemistry, where experimental work is extremely challenging because of the intrinsic difficulties of the experiments themselves and the safety issues associated with this type of chemistry. This thesis is a collection of theoretical studies of actinide chemistry falling into three categories: quantum chemical and matrix isolation studies of small molecules, the electronic structure of organoactinide systems, and uranyl peroxide nanoclusters and other solid state actinide compounds. The work herein not only spans a wide range of systems size but also investigates a range of chemical problems. Various quantum chemical approaches have been employed. Wave function-based methods have been used to study the electronic structure of actinide containing molecules of small to middle-size. Among these methods, the complete active space self consistent field (CASSCF) approach with corrections from second-order perturbation theory (CASPT2), the generalized active space SCF (GASSCF) approach, and Moller-Plesset second-order perturbation theory (MP2) have been employed. Likewise, density functional theory (DFT) has been used along with analysis tools like bond energy decomposition, bond orders, and Bader's Atoms in Molecules. From these quantum chemical results, comparison with experimentally obtained structures and spectra are made.

  13. Toward Accurate Modelling of Enzymatic Reactions: All Electron Quantum Chemical Analysis combined with QM/MM Calculation of Chorismate Mutase

    SciTech Connect

    Ishida, Toyokazu

    2008-09-17

    To further understand the catalytic role of the protein environment in the enzymatic process, the author has analyzed the reaction mechanism of the Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM). By introducing a new computational strategy that combines all-electron QM calculations with ab initio QM/MM modelings, it was possible to simulate the molecular interactions between the substrate and the protein environment. The electrostatic nature of the transition state stabilization was characterized by performing all-electron QM calculations based on the fragment molecular orbital technique for the entire enzyme.

  14. Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

    PubMed

    Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

    2013-04-01

    The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach.

  15. A chemically driven quantum phase transition in a two-molecule Kondo system

    NASA Astrophysics Data System (ADS)

    Esat, Taner; Lechtenberg, Benedikt; Deilmann, Thorsten; Wagner, Christian; Krüger, Peter; Temirov, Ruslan; Rohlfing, Michael; Anders, Frithjof B.; Tautz, F. Stefan

    2016-09-01

    The magnetic properties of nanostructures that consist of a small number of atoms or molecules are typically determined by magnetic exchange interactions. Here, we show that non-magnetic, chemical interactions can have a similarly decisive effect if spin-moment-carrying orbitals extend in space and therefore allow the direct coupling of magnetic properties to wavefunction overlap and the formation of bonding and antibonding orbitals. We demonstrate this for a dimer of metal-molecule complexes on the Au(111) surface. A changing wavefunction overlap between the two monomers drives the surface-adsorbed dimer through a quantum phase transition from an underscreened triplet to a singlet ground state, with one configuration being located extremely close to a quantum critical point.

  16. Quantum-chemical investigations of spectroscopic properties of a fluorescence probe

    NASA Astrophysics Data System (ADS)

    Titova, T. Yu.; Morozova, Yu. P.; Zharkova, O. M.; Artyukhov, V. Ya.; Korolev, B. V.

    2012-09-01

    The prodan molecule (6-propionyl-2-dimethylamino naphthalene) - fluorescence probe - is investigated by quantum-chemical methods of intermediate neglect of differential overlap (INDO) and molecular electrostatic potential (MEP). The dipole moments of the ground and excited states, the nature and position of energy levels, the centers of specific solvation, the rate constants of photoprocesses, and the fluorescence quantum yield are estimated. To elucidate the role of the dimethylamino group in the formation of bands and spectral characteristics, the molecule only with the propionyl group (pron) is investigated. The long-wavelength absorption bands of prodan and pron molecules are interpreted. The results obtained for the prodan molecule by the INDO method with original spectroscopic parameterization are compared with the literature data obtained by the DFT/CIS, ZINDO/S, and AM1/CISD methods.

  17. Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis.

    PubMed

    Allehyani, Basmah H; Elroby, Shaaban A; Aziz, Saadalluh G; Hilal, Rifaat H

    2015-01-01

    This study aims to identify the origin of the extra stability of alloxan, a biologically active pyrimidine. To achieve this goal, detailed DFT computations and quantum dynamics simulations have been performed to establish the most stable conformation and the global minimum structure on the alloxan potential energy surface. The effects of the solvent, basis set, and DFT method have been examined to validate the theoretical model adopted throughout the work. Two non-covalent intermolecular dimers of alloxan, the H-bonded and dipolar dimers, have been investigated at the ωB97X-D and M06-2X levels of theory using the triple zeta 6-311++G** to establish their relative stability. Quantum chemical topology features and natural bond orbital analysis (NBO) have been performed to identify and characterize the forces that govern the structures and underlie the extra stability of alloxan.

  18. Accurate detection of on-state quantum dot and biomolecules in a microfluidic flow with single-molecule two-color coincidence detection.

    PubMed

    Zhang, Chun-Yang; Yang, Kun

    2010-05-01

    Due to their unique optical and electronic properties, quantum dots (QDs) have been widely used in a variety of biosensors for sensitive detection of biomarkers and small molecules. However, single QD exhibits dynamic fluctuation of fluorescence intensity (i.e., blinking) with the transition between on and off states, which adversely influences the development of QD-based optical biosensors. Therefore, the methods for efficient evaluation of on-state QD are especially important and highly desirable. In this paper, a novel and unique approach based on single-molecule two-color coincidence detection is developed to simply and accurately evaluate the on-state QDs in a microfluidic flow. Our results demonstrate that improved QDs in the on state are detected in a microfluidic flow in comparison with that in the Brownian motion state, thus paving the way to the development of single QD-based biosensors for sensitive detection of low-abundance biomolecules. This single-molecule two-color coincidence detection has been applied for the homegeneous detection of nucleic acids in a microfluidic flow with the detection sensitivity of 5.0 fM.

  19. Communication: Ro-vibrational control of chemical reactivity in H+CH{sub 4}→ H{sub 2}+CH{sub 3} : Full-dimensional quantum dynamics calculations and a sudden model

    SciTech Connect

    Welsch, Ralph Manthe, Uwe

    2014-08-07

    The mode-selective chemistry of the title reaction is studied by full-dimensional quantum dynamics simulation on an accurate ab initio potential energy surface for vanishing total angular momentum. Using a rigorous transition state based approach and multi-configurational time-dependent Hartree wave packet propagation, initial state-selected reaction probabilities for many ro-vibrational states of methane are calculated. The theoretical results are compared with experimental trends seen in reactions of methane. An intuitive interpretation of the ro-vibrational control of the chemical reactivity provided by a sudden model based on the quantum transition state concept is discussed.

  20. Biomimetic, Mild Chemical Synthesis of CdTe-GSH Quantum Dots with Improved Biocompatibility

    PubMed Central

    Pérez-Donoso, José M.; Monrás, Juan P.; Bravo, Denisse; Aguirre, Adam; Quest, Andrew F.; Osorio-Román, Igor O.; Aroca, Ricardo F.; Chasteen, Thomas G.; Vásquez, Claudio C.

    2012-01-01

    Multiple applications of nanotechnology, especially those involving highly fluorescent nanoparticles (NPs) or quantum dots (QDs) have stimulated the research to develop simple, rapid and environmentally friendly protocols for synthesizing NPs exhibiting novel properties and increased biocompatibility. In this study, a simple protocol for the chemical synthesis of glutathione (GSH)-capped CdTe QDs (CdTe-GSH) resembling conditions found in biological systems is described. Using only CdCl2, K2TeO3 and GSH, highly fluorescent QDs were obtained under pH, temperature, buffer and oxygen conditions that allow microorganisms growth. These CdTe-GSH NPs displayed similar size, chemical composition, absorbance and fluorescence spectra and quantum yields as QDs synthesized using more complicated and expensive methods. CdTe QDs were not freely incorporated into eukaryotic cells thus favoring their biocompatibility and potential applications in biomedicine. In addition, NPs entry was facilitated by lipofectamine, resulting in intracellular fluorescence and a slight increase in cell death by necrosis. Toxicity of the as prepared CdTe QDs was lower than that observed with QDs produced by other chemical methods, probably as consequence of decreased levels of Cd+2 and higher amounts of GSH. We present here the simplest, fast and economical method for CdTe QDs synthesis described to date. Also, this biomimetic protocol favors NPs biocompatibility and helps to establish the basis for the development of new, “greener” methods to synthesize cadmium-containing QDs. PMID:22292028

  1. Include dispersion in quantum chemical modeling of enzymatic reactions: the case of isoaspartyl dipeptidase.

    PubMed

    Zhang, Hai-Mei; Chen, Shi-Lu

    2015-06-01

    The lack of dispersion in the B3LYP functional has been proposed to be the main origin of big errors in quantum chemical modeling of a few enzymes and transition metal complexes. In this work, the essential dispersion effects that affect quantum chemical modeling are investigated. With binuclear zinc isoaspartyl dipeptidase (IAD) as an example, dispersion is included in the modeling of enzymatic reactions by two different procedures, i.e., (i) geometry optimizations followed by single-point calculations of dispersion (approach I) and (ii) the inclusion of dispersion throughout geometry optimization and energy evaluation (approach II). Based on a 169-atom chemical model, the calculations show a qualitative consistency between approaches I and II in energetics and most key geometries, demonstrating that both approaches are available with the latter preferential since both geometry and energy are dispersion-corrected in approach II. When a smaller model without Arg233 (147 atoms) was used, an inconsistency was observed, indicating that the missing dispersion interactions are essentially responsible for determining equilibrium geometries. Other technical issues and mechanistic characteristics of IAD are also discussed, in particular with respect to the effects of Arg233.

  2. (77)Se chemical shift tensor of L-selenocystine: experimental NMR measurements and quantum chemical investigations of structural effects.

    PubMed

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-03-01

    The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine's specialized biological roles, it is of interest to examine their (77)Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state (77)Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information on selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on (77)Se L-selenocystine's chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10-20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of -180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. -90°, the energy costs to alter the dihedral angle in the range from -120° to -60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. (77)Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272 ± 30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3-9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results suggest

  3. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    ERIC Educational Resources Information Center

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  4. Electronic studies of chrysene. Linear and magnetic circular dichroism and quantum chemical calculations

    SciTech Connect

    Spanget-Larsen, J. ); Waluk, J. ); Thulstrup, E.W. )

    1990-03-08

    The electronic transitions of chrysene are investigated by linear dichroism spectroscopy in stretched polyethylene and by magnetic circular dichroism spectroscopy, leading to the assignment of seven excited singlet states below 47,000 cm{sup {minus}1}. One of these has not previously been observed. The linear dichroism data, combined with previously published fluorescence polarization results, lead to precise determination of transition moment directions for five transitions. The experimental results are compared with theoretical predictions with the PPP, LCOAO, CNDO/S, and INDO/S quantum chemical models.

  5. Quantum-chemical study of electronically excited states of protolytic forms of vanillic acid

    NASA Astrophysics Data System (ADS)

    Vusovich, O. V.; Tchaikovskaya, O. N.; Sokolova, I. V.; Vasil'eva, N. Y.

    2015-12-01

    The paper describes an analysis of possible ways of deactivation of electronically excited states of 4-hydroxy- 3-methoxy-benzoic acid (vanillic acid) and its protolytic forms with the use of quantum-chemical methods INDO/S (intermediate neglect of differential overlap with a spectroscopic parameterization) and MEP (molecular electrostatic potential). The ratio of radiative and non-radiative deactivation channels of the electronic excitation energy is established. The rate constants of photophysical processes (internal and intercombination conversions) occurring after the absorption of light in these forms are evaluated.

  6. Formation and thermodynamics of gaseous germanium and tin vanadates: a mass spectrometric and quantum chemical study.

    PubMed

    Shugurov, S M; Panin, A I; Lopatin, S I; Emelyanova, K A

    2015-06-01

    The stabilities of gaseous germanium and tin vanadates were confirmed by high temperature mass spectrometry, and its structures were determined by quantum chemical calculations. A number of gas-phase reactions involving these gaseous salts were studied. On the basis of the equilibrium constants, the standard formation enthalpies of gaseous GeV2O6 (-1520 ± 42 kJ mol(-1)) and SnV2O6 (-1520 ± 43 kJ mol(-1)) were determined at a temperature of 298 K.

  7. Quantum chemical mechanism in parasitic reaction of AlGaN alloys formation

    NASA Astrophysics Data System (ADS)

    Makino, Osamu; Nakamura, Koichi; Tachibana, Akitomo; Tokunaga, Hiroki; Akutsu, Nakao; Matsumoto, Koh

    2000-06-01

    The mechanism of parasitic reactions among trimethylaluminum (TMA), trimethylgallium (TMG), and NH 3 in atmospheric pressure (AP) MOVPE for growth of AlGaN is theoretically studied using the quantum chemical method. The calculations show that metal-nitrogen chain growth reaction easily proceeds through the successive reactions of 'complex formation with NH 3' and 'CH 4 elimination by the bimolecular mechanism'. Additionally, a parasitic reaction in APMOVPE using other raw material is also investigated. The calculated result shows that small change of raw material raises activation energy of parasitic reaction, and, thus, the parasitic reaction is suppressed. This result suggests a way to improve APMOVPE by a suitable choice of substituent.

  8. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

    PubMed

    Swails, Jason; Zhu, Tong; He, Xiao; Case, David A

    2015-10-01

    We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

  9. Quantum theory of chemical reactions in the presence of electromagnetic fields.

    PubMed

    Tscherbul, T V; Krems, R V

    2008-07-21

    We present a theory for rigorous quantum scattering calculations of probabilities for chemical reactions of atoms with diatomic molecules in the presence of an external electric field. The approach is based on the fully uncoupled basis set representation of the total wave function in the space-fixed coordinate frame, the Fock-Delves hyperspherical coordinates, and the adiabatic partitioning of the total Hamiltonian of the reactive system. The adiabatic channel wave functions are expanded in basis sets of hyperangular functions corresponding to different reaction arrangements, and the interactions with external fields are included in each chemical arrangement separately. We apply the theory to examine the effects of electric fields on the chemical reactions of LiF molecules with H atoms and HF molecules with Li atoms at low temperatures and show that electric fields may enhance the probability of chemical reactions and modify reactive scattering resonances by coupling the rotational states of the reactants. Our preliminary results suggest that chemical reactions of polar molecules at temperatures below 1 K can be selectively manipulated with dc electric fields and microwave laser radiation.

  10. Quantum Chemical Simulations Reveal Acetylene-Based Growth Mechanisms in the Chemical Vapor Deposition Synthesis of Carbon Nanotubes

    SciTech Connect

    Eres, Gyula; Wang, Ying; Gao, Xingfa; Qian, Hu-Jun; Ohta, Yasuhito; Wu, Xiaona; Morokuma, Keiji; Irle, Stephan

    2014-01-01

    Nonequilibrium quantum chemical molecular dynamics (QM/MD) simulation of early stages in the nucleation process of carbon nanotubes from acetylene feedstock on an Fe38 cluster was performed based on the density-functional tight-binding (DFTB) potential. Representative chemical reactions were studied by complimentary static DFTB and density functional theory (DFT) calculations. Oligomerization and cross-linking reactions between carbon chains were found as the main reaction pathways similar to that suggested in previous experimental work. The calculations highlight the inhibiting effect of hydrogen for the condensation of carbon ring networks, and a propensity for hydrogen disproportionation, thus enriching the hydrogen content in already hydrogen-rich species and abstracting hydrogen content in already hydrogen-deficient clusters. The ethynyl radical C2H was found as a reactive, yet continually regenerated species, facilitating hydrogen transfer reactions across the hydrocarbon clusters. The nonequilibrium QM/MD simulations show the prevalence of a pentagon-first nucleation mechanism where hydrogen may take the role of one arm of an sp2 carbon Y-junction. The results challenge the importance of the metal carbide formation for SWCNT cap nucleation in the VLS model and suggest possible alternative routes following hydrogen-abstraction acetylene addition (HACA)-like mechanisms commonly discussed in combustion synthesis.

  11. The nature of resonance-assisted hydrogen bonds: a quantum chemical topology perspective.

    PubMed

    Guevara-Vela, José Manuel; Romero-Montalvo, Eduardo; Costales, Aurora; Pendás, Ángel Martín; Rocha-Rinza, Tomás

    2016-10-14

    Resonance Assisted Hydrogen Bonds (RAHBs) are particularly strong H-Bonds (HBs) which are relevant in several fields of chemistry. The traditional explanation for the occurrence of these HBs is built on mesomeric structures evocative of electron delocalisation in the system. Nonetheless, there are several theoretical studies which have found no evidence of such electron delocalisation. We considered the origin of RAHBs by employing Quantum Chemical Topology tools, more specifically, the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms energy partition. Our results indicate that the π-conjugated bonds allow for a larger adjustment of electron density throughout the H-bonded system as compared with non-conjugated carbonyl molecules. This rearrangement of charge distribution is a response to the electric field due to the H atom involved in the hydrogen bonding of the considered compounds. As opposed to the usual description of RAHB interactions, these HBs lead to a larger electron localisation in the system, and concomitantly to larger QTAIM charges which in turn lead to stronger electrostatic, polarization and charge transfer components of the interaction. Overall, the results presented here offer a new perspective on the cause of strengthening of these important interactions.

  12. Description of Polar Chemical Bonds from the Quantum Mechanical Interference Perspective.

    PubMed

    Fantuzzi, Felipe; Nascimento, Marco Antonio Chaer

    2014-06-10

    The Generalized Product Function Energy Partitioning (GPF-EP) method has been applied to a set of molecules, AH (A = Li, Be, B, C, N, O, F), CO and LiF with quite different dipole moments, in order to investigate the role played by the quantum interference effect in the formation of polar chemical bonds. The calculations were carried out with GPF wave functions treating all the core electrons as a single Hartree-Fock group and the bonding electrons at the Generalized Valence Bond Perfect-Pairing (GVB-PP) level, with the cc-pVTZ basis set. The results of the energy partitioning into interference and quasi-classical contributions along the respective Potential Energy Surfaces (PES) show that the main contribution to the depth of the potential wells comes from the interference term, which is an indication that all the molecules mentioned above form typical covalent bonds. In all cases, the stabilization promoted by the interference term comes from the kinetic contribution, in agreement with previous results. The analysis of the effect of quantum interference on the electron density reveals that while polarization effects (quasi-classical) tend to displace electronic density from the most polarizable atom toward the less polarizable one, interference (quantum effects) counteracts by displacing electronic density to the bond region, giving rise to the right electronic density and dipole moment.

  13. Graphenol defects induced blue emission enhancement in chemically reduced graphene quantum dots.

    PubMed

    Zhang, Wenkai; Liu, Yingqiu; Meng, Xianrui; Ding, Tao; Xu, Yuanqing; Xu, Hao; Ren, Yanrong; Liu, Baoying; Huang, Jiajia; Yang, Jinghe; Fang, Xiaomin

    2015-09-14

    In this work, few layer graphene quantum dots (GQDs) with a size of 3-5 nm are purposely treated with highly concentrated aqueous NaBH4 solutions to obtain the reduced graphene quantum dots (rGQDs). Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy demonstrate that the number of carbonyl groups decreases but -OH related defects increase during chemical reduction. Green and weak emissions of original GQDs originate from carrier recombination in the disorder-induced localized state (mainly including carbonyl and carboxyl and epoxy groups). As the reduction degree increases, the photoluminescence (PL) quantum efficiency of GQDs increases dramatically from 2.6% to 10.1%. In the meantime, the PL peak position blue shifts rapidly, and full width at half maximum (FWHM) becomes narrower. Thus we can infer that graphenol topological defects (hydroxyl functionalized graphene) are gradually formed during reduction. Besides, graphenol defect related PL features a longer fluorescence lifetime, excitation wavelength dependence but less pH sensitivity. PMID:26247890

  14. Influence of wet chemical cleaning on quantum efficiency of GaN photocathode

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Hui; Gao, Pin; Wang, Hong-Gang; Li, Biao; Chang, Ben-Kang

    2013-02-01

    GaN samples 1-3 are cleaned by a 2:2:1 solution of sulfuric acid (98%) to hydrogen peroxide (30%) to de-ionized water; hydrochloric acid (37%); or a 4:1 solution of sulfuric acid (98%) to hydrogen peroxide (30%). The samples are activated by Cs/O after the same annealing process. X-ray photoelectron spectroscopy after the different ways of wet chemical cleaning shows: sample 1 has the largest proportion of Ga, N, and O among the three samples, while its C content is the lowest. After activation the quantum efficiency curves show sample 1 has the best photocathode performance. We think the wet chemical cleaning method is a process which will mainly remove C contamination.

  15. Probing silicon and aluminium chemical environments in silicate and aluminosilicate glasses by solid state NMR spectroscopy and accurate first-principles calculations

    NASA Astrophysics Data System (ADS)

    Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Caurant, Daniel; Charpentier, Thibault

    2014-01-01

    Silicon and aluminium chemical environments in silicate and aluminosilicate glasses with compositions 60SiO2·20Na2O·20CaO (CSN), 60SiO2·20Al2O3·20CaO (CAS), 78SiO2·11Al2O3·11Na2O (NAS) and 60SiO2·10Al2O3·10Na2O·20CaO (CASN) have been investigated by 27Al and 29Si solid state magic angle spinning (MAS) and multiple quantum MAS (MQMAS) nuclear magnetic resonance (NMR) experiments. To interpret the NMR data, first-principles calculations using density functional theory were performed on structural models of these glasses. These models were generated by Shell-model molecular dynamics (MD) simulations. The theoretical NMR parameters and spectra were computed using the gauge including projected augmented wave (GIPAW) method and spin-effective Hamiltonians, respectively. This synergetic computational-experimental approach offers a clear structural characterization of these glasses, particularly in terms of network polymerization, chemical disorder (i.e. Si and Al distribution in second coordination sphere) and modifier cation distributions. The relationships between the local structural environments and the 29Si and 27Al NMR parameters are highlighted, and show that: (i) the isotropic chemical shift of both 29Si and 27Al increases of about +5 ppm for each Al added in the second sphere and (ii) both the 27Al and 29Si isotropic chemical shifts linearly decrease with the reduction of the average Si/Al-O-T bond angle. Conversely, 27Al and 29Si NMR parameters are much less sensitive to the connectivity with triple bridging oxygen atoms, precluding their indirect detection from 27Al and 29Si NMR.

  16. Quantum chemical study of Co3+ spin states in LaCoO3

    NASA Astrophysics Data System (ADS)

    Siurakshina, L.; Paulus, B.; Yushankhai, V.; Sivachenko, E.

    2010-03-01

    Ab initio quantum-chemical cluster calculations are performed for the perovskite LaCoO3. The main concern is to calculate the energy level ordering of different spin states of Co3+, which is an issue of great controversy for many years. The calculations performed for the trigonal lattice structure at T = 5 K and 300 K, with the structural data taken from experiment, display that the low-spin (LS, S = 0) ground state is separated from the first excited high-spin (HS, S = 2) state by a gap <100 meV, while the intermediate-spin (IS, S = 1) state is located at much higher energy ≈0.5 eV. We suggest that the local lattice relaxation around the Co3+ ion excited to the HS state and the spin-orbit coupling reduce the spin gap to a value 10 meV. Coupling of the IS state to the Jahn-Teller local lattice distortion is found to be rather strong and reduces its energy position to a value of 200 div 300 meV. Details of the quantum-chemical cluster calculation procedure and the obtained results are extensively discussed and compared with those reported earlier by other authors.

  17. Prediction of contaminant persistence in aqueous phase: a quantum chemical approach.

    PubMed

    Blotevogel, Jens; Mayeno, Arthur N; Sale, Tom C; Borch, Thomas

    2011-03-15

    At contaminated field sites where active remediation measures are not feasible, monitored natural attenuation is sometimes the only alternative for surface water or groundwater decontamination. However, due to slow degradation rates of some contaminants under natural conditions, attenuation processes and their performance assessment can take several years to decades to complete. Here, we apply quantum chemical calculations to predict contaminant persistence in the aqueous phase. For the test compound hexamethylphosphoramide (HMPA), P-N bond hydrolysis is the only thermodynamically favorable reaction that may lead to its degradation under reducing conditions. Through calculation of aqueous Gibbs free energies of activation for all potential reaction mechanisms, it is predicted that HMPA hydrolyzes via an acid-catalyzed mechanism at pH < 8.2, and an uncatalyzed mechanism at pH 8.2-8.5. The estimated half-lives of thousands to hundreds of thousands of years over the groundwater-typical pH range of 6.0 to 8.5 indicate that HMPA will be persistent in the absence of suitable oxidants. At pH 0, where the hydrolysis reaction is rapid enough to enable measurement, the experimentally determined rate constant and half-life are in excellent agreement with the predicted values. Since the quantum chemical methodology described herein can be applied to virtually any contaminant or reaction of interest, it is especially valuable for the prediction of persistence when slow reaction rates impede experimental investigations and appropriate QSARs are unavailable.

  18. Quantum chemical approach to study the spectral properties of some important precursor of bio-molecules

    NASA Astrophysics Data System (ADS)

    Majumdar, Liton; Das, Ankan; Chakrabarti, Sandip K.; Chakrabarti, Sonali

    2013-06-01

    This work reports the spectral information of some interstellar complex molecules which could be treated as the precursor molecules for the formation of some bio-molecules in the interstellar medium (ISM). We carry out quantum chemical simulation to consider the Core correlation and vibrational corrections to the rotational constants and centrifugal distortion constants which are computed from harmonic and anharmonic force fields obtained at MP2/6-311G(d,p) level of theory. These precursor molecules could be produced in the gas phase as well as in the ice phase. This prompted use to couple the hydrodynamics of the collapsing phase of the protostar with our reasonably large chemical network including the gas phase as well as the grain phase chemical network, to study the chemical evolution of these species during the collapsing phase of a proto-star. We have noticed the Significant differences between spectroscopy of these species in the gas as well as in ice (water ice) phase due to the solute-solvent elctrostatic interactions. Time dependent density functional theory (TDDFT) is used to study the UV-VIS spectrum of these complexmolecules which are biologically important. Interstellar grain mantle around the dense cloud (> 104 cm-3) mainly composed by 60-70% Water, 5-30% Methanol and 2-20% CO2. So in reality, the ice could be mixed instead of simple water ice. To have an idea about the real spectra, we carry out our simulations for the mixed ice also by considering the actual composition of the above species in interstellar grain mantle. Spectral signatures are found to be significantly shifted with change of the solvent which confirms that the polarization of the solute by the continum has important effects on the absolute and relative solvation energies. Our simulated spectrum are in good agreement with some of the recent experimental result. We expect that our quantum chemical approach along with the hydro-chemical study might be useful for the observer to

  19. Coherent chemical kinetics as quantum walks. I. Reaction operators for radical pairs.

    PubMed

    Chia, A; Tan, K C; Pawela, Ł; Kurzyński, P; Paterek, T; Kaszlikowski, D

    2016-03-01

    Classical chemical kinetics uses rate-equation models to describe how a reaction proceeds in time. Such models are sufficient for describing state transitions in a reaction where coherences between different states do not arise, in other words, a reaction that contains only incoherent transitions. A prominent example of a reaction containing coherent transitions is the radical-pair model. The kinetics of such reactions is defined by the so-called reaction operator that determines the radical-pair state as a function of intermediate transition rates. We argue that the well-known concept of quantum walks from quantum information theory is a natural and apt framework for describing multisite chemical reactions. By composing Kraus maps that act only on two sites at a time, we show how the quantum-walk formalism can be applied to derive a reaction operator for the standard avian radical-pair reaction. Our reaction operator predicts the same recombination dephasing rate as the conventional Haberkorn model, which is consistent with recent experiments [K. Maeda et al., J. Chem. Phys. 139, 234309 (2013)], in contrast to previous work by Jones and Hore [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010)]. The standard radical-pair reaction has conventionally been described by either a normalized density operator incorporating both the radical pair and reaction products or a trace-decreasing density operator that considers only the radical pair. We demonstrate a density operator that is both normalized and refers only to radical-pair states. Generalizations to include additional dephasing processes and an arbitrary number of sites are also discussed.

  20. Under proper control, oxidation of proteins with known chemical structure provides an accurate and absolute method for the determination of their molar concentration.

    PubMed

    Guermant, C; Azarkan, M; Smolders, N; Baeyens-Volant, D; Nijs, M; Paul, C; Brygier, J; Vincentelli, J; Looze, Y

    2000-01-01

    Oxidation at 120 degrees C of inorganic and organic (including amino acids, di- and tripeptides) model compounds by K(2)Cr(2)O(7) in the presence of H(2)SO(4) (mass fraction: 0.572), Ag(2)SO(4) (catalyst), and HgSO(4) results in the quantitative conversion of their C-atoms into CO(2) within 24 h or less. Under these stressed, well-defined conditions, the S-atoms present in cysteine and cystine residues are oxidized into SO(3) while, interestingly, the oxidation states of all the other (including the N-) atoms normally present in a protein do remain quite unchanged. When the chemical structure of a given protein is available, the total number of electrons the protein is able to transfer to K(2)Cr(2)O(7) and thereof, the total number of moles of Cr(3+) ions which the protein is able to generate upon oxidation can be accurately calculated. In such cases, unknown protein molar concentrations can thus be determined through straightforward spectrophotometric measurements of Cr(3+) concentrations. The values of molar absorption coefficients for several well-characterized proteins have been redetermined on this basis and observed to be in excellent agreement with the most precise values reported in the literature, which fully assesses the validity of the method. When applied to highly purified proteins of known chemical structure (more generally of known atomic composition), this method is absolute and accurate (+/-1%). Furthermore, it is well adapted to series measurements since available commercial kits for chemical oxygen demand (COD) measurements can readily be adapted to work under the experimental conditions recommended here for the protein assay. PMID:10610688

  1. Efficient Implementation of Many-body Quantum Chemical Methods on the Intel Xeon Phi Coprocessor

    SciTech Connect

    Apra, Edoardo; Klemm, Michael; Kowalski, Karol

    2014-12-01

    This paper presents the implementation and performance of the highly accurate CCSD(T) quantum chemistry method on the Intel Xeon Phi coprocessor within the context of the NWChem computational chemistry package. The widespread use of highly correlated methods in electronic structure calculations is contingent upon the interplay between advances in theory and the possibility of utilizing the ever-growing computer power of emerging heterogeneous architectures. We discuss the design decisions of our implementation as well as the optimizations applied to the compute kernels and data transfers between host and coprocessor. We show the feasibility of adopting the Intel Many Integrated Core Architecture and the Intel Xeon Phi coprocessor for developing efficient computational chemistry modeling tools. Remarkable scalability is demonstrated by benchmarks. Our solution scales up to a total of 62560 cores with the concurrent utilization of Intel Xeon processors and Intel Xeon Phi coprocessors.

  2. Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors.

    PubMed

    Schirmeister, Tanja; Kesselring, Jochen; Jung, Sascha; Schneider, Thomas H; Weickert, Anastasia; Becker, Johannes; Lee, Wook; Bamberger, Denise; Wich, Peter R; Distler, Ute; Tenzer, Stefan; Johé, Patrick; Hellmich, Ute A; Engels, Bernd

    2016-07-13

    We propose a structure-based protocol for the development of customized covalent inhibitors. Starting from a known inhibitor, in the first and second steps appropriate substituents of the warhead are selected on the basis of quantum mechanical (QM) computations and hybrid approaches combining QM with molecular mechanics (QM/MM). In the third step the recognition unit is optimized using docking approaches for the noncovalent complex. These predictions are finally verified by QM/MM or molecular dynamic simulations. The applicability of our approach is successfully demonstrated by the design of reversible covalent vinylsulfone-based inhibitors for rhodesain. The examples show that our approach is sufficiently accurate to identify compounds with the desired properties but also to exclude nonpromising ones.

  3. Computer simulations of local anesthetic mechanisms: Quantum chemical investigation of procaine

    SciTech Connect

    Smith, Jeremy C; Bondar, A.N.; Suhai, Sandor; Frangopol, P.T.

    2007-02-01

    A description at the atomic level of detail of the interaction between local anesthetics, lipid membranes and membrane proteins, is essential for understanding the mechanism of local anesthesia. The importance of performing computer simulations to decipher the mechanism of local anesthesia is discussed here in the context of the current status of understanding of the local anesthetics action. As a first step towards accurate simulations of the interaction between local anesthetics, proteins, lipid and water molecules, here we use quantum mechanical methods to assess the charge distribution and structural properties of procaine in the presence and in the absence of water molecules. The calculations indicate that, in the absence of hydrogen-bonding water molecules, protonated procaine strongly prefers a compact structure enabled by intramolecular hydrogen bonding. In the presence of water molecules the torsional energy pro?le of procaine is modified, and hydrogen bonding to water molecules is favored relative to intra-molecular hydrogen bonding.

  4. Degradation of di(2-ethyl hexyl) phthalate by Fusarium culmorum: Kinetics, enzymatic activities and biodegradation pathway based on quantum chemical modelingpathway based on quantum chemical modeling.

    PubMed

    Ahuactzin-Pérez, Miriam; Tlecuitl-Beristain, Saúl; García-Dávila, Jorge; González-Pérez, Manuel; Gutiérrez-Ruíz, María Concepción; Sánchez, Carmen

    2016-10-01

    Di(2-ethylhexyl) phthalate (DEHP) is a plasticizer widely used in the manufacture of plastics, and it is an environmental contaminant. The specific growth rate (μ), maximum biomass (Xmax), biodegradation constant of DEHP (k), half-life (t1/2) of DEHP biodegradation and removal efficiency of DEHP, esterase and laccase specific activities, and enzymatic yield parameters were evaluated for Fusarium culmorum grown on media containing glucose and different concentrations of DEHP (0, 500 and 1000mg/L). The greatest μ and the largest Xmax occurred in media supplemented with 1000mg of DEHP/L. F. culmorum degraded 95% of the highest amount of DEHP tested (1000mg/L) within 60h of growth. The k and t1/2 were 0.024h(-1) and 28h, respectively, for both DEHP concentrations. The removal efficiency of DEHP was 99.8% and 99.9% for 1000 and 500mg/L, respectively. Much higher specific esterase activity than specific laccase activity was observed in all media tested. The compounds of biodegradation of DEHP were identified by GC-MS. A DEHP biodegradation pathway by F. culmorum was proposed on the basis of the intermolecular flow of electrons of the identified intermediate compounds using quantum chemical modeling. DEHP was fully metabolized by F. culmorum with butanediol as the final product. This fungus offers great potential in bioremediation of environments polluted with DEHP.

  5. A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules

    NASA Astrophysics Data System (ADS)

    Stauch, Tim; Dreuw, Andreas

    2014-04-01

    The promising field of mechanochemistry suffers from a general lack of understanding of the distribution and propagation of force in a stretched molecule, which limits its applicability up to the present day. In this article, we introduce the JEDI (Judgement of Energy DIstribution) analysis, which is the first quantum chemical method that provides a quantitative understanding of the distribution of mechanical stress energy among all degrees of freedom in a molecule. The method is carried out on the basis of static or dynamic calculations under the influence of an external force and makes use of a Hessian matrix in redundant internal coordinates (bond lengths, bond angles, and dihedral angles), so that all relevant degrees of freedom of a molecule are included and mechanochemical processes can be interpreted in a chemically intuitive way. The JEDI method is characterized by its modest computational effort, with the calculation of the Hessian being the rate-determining step, and delivers, except for the harmonic approximation, exact ab initio results. We apply the JEDI analysis to several example molecules in both static quantum chemical calculations and Born-Oppenheimer Molecular Dynamics simulations in which molecules are subject to an external force, thus studying not only the distribution and the propagation of strain in mechanically deformed systems, but also gaining valuable insights into the mechanochemically induced isomerization of trans-3,4-dimethylcyclobutene to trans,trans-2,4-hexadiene. The JEDI analysis can potentially be used in the discussion of sonochemical reactions, molecular motors, mechanophores, and photoswitches as well as in the development of molecular force probes.

  6. A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules

    SciTech Connect

    Stauch, Tim; Dreuw, Andreas

    2014-04-07

    The promising field of mechanochemistry suffers from a general lack of understanding of the distribution and propagation of force in a stretched molecule, which limits its applicability up to the present day. In this article, we introduce the JEDI (Judgement of Energy DIstribution) analysis, which is the first quantum chemical method that provides a quantitative understanding of the distribution of mechanical stress energy among all degrees of freedom in a molecule. The method is carried out on the basis of static or dynamic calculations under the influence of an external force and makes use of a Hessian matrix in redundant internal coordinates (bond lengths, bond angles, and dihedral angles), so that all relevant degrees of freedom of a molecule are included and mechanochemical processes can be interpreted in a chemically intuitive way. The JEDI method is characterized by its modest computational effort, with the calculation of the Hessian being the rate-determining step, and delivers, except for the harmonic approximation, exact ab initio results. We apply the JEDI analysis to several example molecules in both static quantum chemical calculations and Born-Oppenheimer Molecular Dynamics simulations in which molecules are subject to an external force, thus studying not only the distribution and the propagation of strain in mechanically deformed systems, but also gaining valuable insights into the mechanochemically induced isomerization of trans-3,4-dimethylcyclobutene to trans,trans-2,4-hexadiene. The JEDI analysis can potentially be used in the discussion of sonochemical reactions, molecular motors, mechanophores, and photoswitches as well as in the development of molecular force probes.

  7. Characteristics of the complexing of chitosan with sodium dodecyl sulfate, according to IR spectroscopy data and quantum-chemical calculations

    NASA Astrophysics Data System (ADS)

    Shilova, S. V.; Romanova, K. A.; Galyametdinov, Yu. G.; Tret'yakova, A. Ya.; Barabanov, V. P.

    2016-06-01

    The complexing of protonated chitosan with dodecyl sulfate ions in water solutions is studied using IR spectroscopy data and quantum-chemical calculations. It is established that the electrostatic interaction between the protonated amino groups of chitosan and dodecyl sulfate ions is apparent in the IR spectrum as a band at 833 cm-1. The need to consider the effect the solvent has on the formation of hydrogen-bound ion pairs [CTS+ ṡ C12H25O 3 - ] is shown via a quantum-chemical simulation of the equilibrium geometry and the energy characteristics of complexing and hydration.

  8. Effect of chemical fixatives on accurate preservation of Escherichia coli and Bacillus subtilis structure in cells prepared by freeze-substitution

    SciTech Connect

    Graham, L.L.; Beveridge, T.J. )

    1990-04-01

    Five chemical fixatives were evaluated for their ability to accurately preserve bacterial ultrastructure during freeze-substitution of select Escherichia coli and Bacillus subtilis strains. Radioisotopes were specifically incorporated into the peptidoglycan, lipopolysaccharide, and nucleic acids of E. coli SFK11 and W7 and into the peptidoglycan and RNA of B. subtilis 168 and W23. The ease of extraction of radiolabels, as assessed by liquid scintillation counting during all stages of processing for freeze-substitution, was used as an indicator of cell structural integrity and retention of cellular chemical composition. Subsequent visual examination by electron microscopy was used to confirm ultrastructural conformation. The fixatives used were: 2% (wt/vol) osmium tetroxide and 2% (wt/vol) uranyl acetate; 2% (vol/vol) glutaraldehyde and 2% (wt/vol) uranyl acetate; 2% (vol/vol) acrolein and 2% (wt/vol) uranyl acetate; 2% (wt/vol) gallic acid; and 2% (wt/vol) uranyl acetate. All fixatives were prepared in a substitution solvent of anhydrous acetone. Extraction of cellular constituents depended on the chemical fixative used. A combination of 2% osmium tetroxide-2% uranyl acetate or 2% gallic acid alone resulted in optimum fixation as ascertained by least extraction of radiolabels. In both gram-positive and gram-negative organisms, high levels of radiolabel were detected in the processing fluids in which 2% acrolein-2% uranyl acetate, 2% glutaraldehyde-2% uranyl acetate, or 2% uranyl acetate alone were used as fixatives. Ultrastructural variations were observed in cells freeze-substituted in the presence of different chemical fixatives. We recommend the use of osmium tetroxide and uranyl acetate in acetone for routine freeze-substitution of eubacteria, while gallic acid is recommended for use when microanalytical processing necessitates the omission of osmium.

  9. Photophysical and quantum chemical studies on the interactions of oxazine-1 dye with cucurbituril macrocycles.

    PubMed

    Sayed, Mhejabeen; Sundararajan, Mahesh; Mohanty, Jyotirmayee; Bhasikuttan, Achikanath C; Pal, Haridas

    2015-02-19

    Supramolecular host-guest interaction of cationic oxazine-1 (OX1) dye with two cucurbit[n]uril (CBn) hosts, namely, CB7 and CB8, has been investigated using photophysical and quantum chemical studies. Both CB7 and CB8 display much stronger binding affinities for OX1 dye compared to conventional cyclodextrin (CD) hosts, which arises due to strong ion-dipole interaction in stabilizing the dye-host inclusion complexes in the present systems. From photophysical studies supported by (1)H NMR results and quantum chemical calculations, it is inferred that 1:1 inclusion complexes are mainly formed in the present systems, though a small percentage of 1:2 (dye·host2) complexes are also indicated from time-resolved (TR) fluorescence studies. Longer rotational relaxation times for dye-CBn systems compared to the free dye as estimated from TR anisotropy studies support the inclusion complex formation in the present systems. The binding constant value is estimated to be significantly higher for the OX1-CB7 system than the OX1-CB8 system, and these results are in accordance with compatible portal diameter of CB7 cavity compared to the much larger portal diameter of CB8 cavity relative to the width of the OX1 molecule. Accordingly, CB7 cavity renders a relatively stronger binding than the CB8 cavity for an axially incorporated OX1 dye into the host cavity. Results from the quantum chemical calculations are overall supportive to the inferences drawn from photophysical measurements. Observed results clearly suggest that the dimensions of the CBn cavities play an important role in determining the interaction strength and stoichiometry of the host-guest complexes formed and thus bring out significant changes in the photophysical properties of the bound dye. The host-assisted modulation in the photophysical properties of the dye, as observed in the present study, has a direct relevance to applications like aqueous dye lasers, sensors, fluorescence assays, and so on.

  10. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    SciTech Connect

    Xu, Zhongnan; Kitchin, John R.; Joshi, Yogesh V.; Raman, Sumathy

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  11. Toward the realization of a compact chemical sensor platform using quantum cascade lasers

    NASA Astrophysics Data System (ADS)

    Holthoff, Ellen L.; Marcus, Logan S.; Pellegrino, Paul M.

    2015-05-01

    The Army is investigating several spectroscopic techniques (e.g., infrared spectroscopy) that could allow for an adaptable sensor platform. Traditionally, chemical sensing platforms have been hampered by the opposing concerns of increasing sensor capability while maintaining a minimal package size. Current sensors, although reasonably sized, are geared to more classical chemical threats, and the ability to expand their capabilities to a broader range of emerging threats is uncertain. Recently, photoacoustic spectroscopy, employed in a sensor format, has shown enormous potential to address these ever-changing threats, while maintaining a compact sensor design. In order to realize the advantage of photoacoustic sensor miniaturization, light sources of comparable size are required. Recent research has employed quantum cascade lasers (QCLs) in combination with MEMS-scale photoacoustic cell designs. The continuous tuning capability of QCLs over a broad wavelength range in the mid-infrared spectral region greatly expands the number of compounds that can be identified. Results have demonstrated that utilizing a tunable QCL with a MEMS-scale photoacoustic cell produces favorable detection limits (ppb levels) for chemical targets (e.g., dimethyl methyl phosphonate (DMMP), vinyl acetate, 1,4-dioxane). Although our chemical sensing research has benefitted from the broad tuning capabilities of QCLs, the limitations of these sources must be considered. Current commercially available tunable systems are still expensive and obviously geared more toward laboratory operation, not fielding. Although the laser element itself is quite small, the packaging, power supply, and controller remain logistical burdens. Additionally, operational features such as continuous wave (CW) modulation and laser output powers while maintaining wide tunability are not yet ideal for a variety of sensing applications. In this paper, we will discuss our continuing evaluation of QCL technology as it matures

  12. Quantum Dot and Polymer Composite Cross-Reactive Array for Chemical Vapor Detection.

    PubMed

    Bright, Collin J; Nallon, Eric C; Polcha, Michael P; Schnee, Vincent P

    2015-12-15

    A cross-reactive chemical sensing array was made from CdSe Quantum Dots (QDs) and five different organic polymers by inkjet printing to create segmented fluorescent composite regions on quartz substrates. The sensor array was challenged with exposures from two sets of analytes, including one set of 14 different functionalized benzenes and one set of 14 compounds related to security concerns, including the explosives trinitrotoluene (TNT) and ammonium nitrate. The array was broadly responsive to analytes with different chemical functionalities due to the multiple sensing mechanisms that altered the QDs' fluorescence. The sensor array displayed excellent discrimination between members within both sets. Classification accuracy of more than 93% was achieved, including the complete discrimination of very similar dinitrobenzene isomers and three halogenated, substituted benzene compounds. The simple fabrication, broad responsivity, and high discrimination capacity of this type of cross-reactive array are ideal qualities for the development of sensors with excellent sensitivity to chemical and explosive threats while maintaining low false alarm rates. PMID:26548712

  13. Structure activity studies of an analgesic drug tapentadol hydrochloride by spectroscopic and quantum chemical methods

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Santhanam, R.; Marchewka, M. K.; Mohan, S.; Yang, Haifeng

    2015-11-01

    Tapentadol is a novel opioid pain reliever drug with a dual mechanism of action, having potency between morphine and tramadol. Quantum chemical calculations have been carried out for tapentadol hydrochloride (TAP.Cl) to determine the properties. The geometry is optimised and the structural properties of the compound were determined from the optimised geometry by B3LYP method using 6-311++G(d,p), 6-31G(d,p) and cc-pVDZ basis sets. FT-IR and FT-Raman spectra are recorded in the solid phase in the region of 4000-400 and 4000-100 cm-1, respectively. Frontier molecular orbital energies, LUMO-HOMO energy gap, ionisation potential, electron affinity, electronegativity, hardness and chemical potential are also calculated. The stability of the molecule arising from hyperconjugative interactions and charge delocalisation has been analysed using NBO analysis. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule are analysed.

  14. Experimental and Quantum-Chemical Study of Electronically Excited States of Protolytic Isovanillin Species

    NASA Astrophysics Data System (ADS)

    Vusovich, O. V.; Tchaikovskaya, O. N.; Sokolova, I. V.; Vasil'eva, N. Yu.

    2014-05-01

    Methods of electronic spectroscopy and quantum chemistry are used to compare protolytic vanillin and isovanillin species. Three protolytic species: anion, cation, and neutral are distinguished in the ground state of the examined molecules. Vanillin and isovanillin in the ground state in water possess identical spectral characteristics: line positions and intensities in the absorption spectra coincide. Minima of the electrostatic potential demonstrate that the deepest isomer minimum is observed on the carbonyl oxygen atom. However, investigations of the fluorescence spectra show that the radiative properties of isomers differ. An analysis of results of quantum-chemical calculations demonstrate that the long-wavelength ππ* transition in the vanillin absorption spectra is formed due to electron charge transfer from the phenol part of the molecule to oxygen atoms of the methoxy and carbonyl groups, and in the isovanillin absorption spectra, it is formed only on the oxygen atom of the methoxy group. The presence of hydroxyl and carbonyl groups in the structure of the examined molecules leads to the fact that isovanillin in the ground S0 state, the same as vanillin, possesses acidic properties, whereas in the excited S1 state, they possess basic properties. A comparison of the рKа values of aqueous solutions demonstrates that vanillin possesses stronger acidic and basic properties in comparison with isovanillin.

  15. Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination.

    PubMed

    de Courcy, Benoit; Derat, Etienne; Piquemal, Jean-Philip

    2015-06-01

    This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the reductive elimination, palladium delocalizes its valence electrons not only toward phosphines but interestingly also toward the carbene. As back-donation increases during reductive elimination, one of the reaction key components is the palladium ligands ability to accept electrons. The rationalization of such electronic phenomena gives new directions for the design of palladium-catalyzed systems. PMID:25899703

  16. Temperature engineered growth of low-threshold quantum well lasers by metalorganic chemical vapor deposition

    SciTech Connect

    Dzurko, K.M.; Menu, E.P.; Beyler, C.A.; Osinski, J.S.; Dapkus, P.D.

    1989-01-09

    A new technique is demonstrated for the formation of narrow active regions in quantum well lasers. In temperature engineered growth (TEG), the substrate temperature is varied during the growth of epitaxial layers by metalorganic chemical vapor deposition (MOCVD) on nonplanar substrates, allowing two-dimensional control of device features. Buried heterostructure designs with submicron active region stripe widths are obtained without the need for fine process control of lateral dimensions. The contact area above the active region is coplanar with the surrounding surface and wide enough to allow easy contacting and heat sinking. Carrier confinement is accomplished by lateral thickness variation of the quantum well active region resulting in a local strip of minimum band gap. Lasers grown in this manner exhibit cw threshold currents as low as 3.8 mA (3.4 mA pulsed), having an as-grown active region width of 0.5 ..mu..m. The near-field optical profile indicates stable, single transverse mode operation and minimal current leakage in these devices.

  17. Quantum Chemical Analysis of MHC-Peptide Interactions for Vaccine Design

    PubMed Central

    Agudelo, W.A; Patarroyo, M.E

    2010-01-01

    The development of an adequate immune response against pathogens is mediated by molecular interactions between different cell types. Among them, binding of antigenic peptides to the Major Histocompatibility Complex (MHC) molecule expressed on the membrane of antigen presenting cells (APCs), and their subsequent recognition by the T cell receptor have been demonstrated to be crucial for developing an adequate immune response. The present review compiles computational quantum chemistry studies about the electrostatic potential variations induced on the MHC binding region by peptide’s amino acids, carried out with the aim of describing MHC–peptide binding interactions. The global idea is that the electrostatic potential can be represented in terms of a series expansion (charge, dipole, quadrupole, hexadecapole, etc.) whose three first terms provide a good local approximation to the molecular electrostatic ‘landscape’ and to the variations induced on such landscape by targeted modifications on the residues of the antigenic peptide. Studies carried out in four MHC class II human allele molecules, which are the most representative alleles of their corresponding haplotypes, showed that each of these molecules have conserved as well as specific electrostatic characteristics, which can be correlated at a good extent with the peptide binding profiles reported experimentally for these molecules. The information provided by such characteristics would help increase our knowledge about antigen binding and presentation, and could ultimately contribute to developing a logical and rational methodology for designing chemically synthesized, multi-antigenic, subunit-based vaccines, through the application of quantum chemistry methods. PMID:20394575

  18. Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination.

    PubMed

    de Courcy, Benoit; Derat, Etienne; Piquemal, Jean-Philip

    2015-06-01

    This article proposes to bridge two fields, namely organometallics and quantum chemical topology. To do so, Palladium-catalyzed reductive elimination is studied. Such reaction is a classical elementary step in organometallic chemistry, where the directionality of electrons delocalization is not well understood. New computational evidences highlighting the accepted mechanism are proposed following a strategy coupling quantum theory of atoms in molecules and electron localization function topological analyses and enabling an extended quantification of donated/back-donated electrons fluxes along reaction paths going beyond the usual Dewar-Chatt-Duncanson model. Indeed, if the ligands coordination mode (phosphine, carbene) is commonly described as dative, it appears that ligands lone pairs stay centered on ligands as electrons are shared between metal and ligand with strong delocalization toward the latter. Overall, through strong trans effects coming from the carbon involved in the reductive elimination, palladium delocalizes its valence electrons not only toward phosphines but interestingly also toward the carbene. As back-donation increases during reductive elimination, one of the reaction key components is the palladium ligands ability to accept electrons. The rationalization of such electronic phenomena gives new directions for the design of palladium-catalyzed systems.

  19. Absorption spectrophotometric, fluorescence, transient absorption and quantum chemical investigations on fullerene/phthalocyanine supramolecular complexes.

    PubMed

    Ray, Anamika; Santhosh, Kotni; Bhattacharya, Sumanta

    2011-05-01

    The present paper reports the photophysical investigations on supramolecular interaction of a phthalocyanine derivative, namely, 2,9,16,23-tetra-tert-butyl-29H,31H-Pc (1) with C(60) and C(70) in toluene. The binding constants of the C(60) and C(70) complexes of 1 are estimated to be 27,360 and 25,205 dm(3), respectively. Transient absorption measurements in the visible region establishes that energy transfer from C60*T (and C70*T) to 1 occurs predominantly in toluene which is subsequently confirmed by the consecutive appearance of the triplet states of 1. Quantum chemical calculations at DFT level of theory explore the geometry and electronic structure of the supramolecules and testify the significant redistribution of charge between fullerenes and 1.

  20. Chemical changes accompanying facet degradation of AlGaAs quantum well lasers

    NASA Astrophysics Data System (ADS)

    Houle, F. A.; Neiman, D. L.; Tang, W. C.; Rosen, H. J.

    1992-11-01

    Detailed measurements are reported using high-resolution scanning Auger microscopy of the chemical state of uncoated quantum well (QW) laser facets after brief and intermediate operating times. Analyses or uncoated facets which have suffered catastrophic optical damage (COD) under various operating conditions are described. The data show clearly that initial facet compositions are variable and far from ideal. After operation for as little as 2-10 min, the composition of the facet regions of the active/graded index and cladding layer change markedly, but no single type of change can be linked to COD. In particular, facet oxidation is not uniform or extensive, and facets which suffer COD are not necessarily more oxidized than those which have not. Composition changes are not limited to the facet surface, indicating that elemental redistribution during laser operation is very fast. These results suggest that the process of facet degradation plays a complex role in laser degradation.

  1. Structural studies on banana oil, isoamyl acetate, by means of microwave spectroscopy and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Sutikdja, L. W.; Jelisavac, D.; Stahl, W.; Kleiner, I.

    2012-12-01

    The rotational spectrum of isoamyl acetate, H3C-COO-(CH2)2-CH(CH3)2, has been recorded and assigned using a molecular beam Fourier transform microwave (MB-FTMW) spectrometer in the frequency range of 3-26.5 GHz. One conformer has been observed. By comparing the spectroscopic data with the quantum chemical data, it was found that the conformer observed does not have Cs symmetry. The rotational and centrifugal distortion constants were determined. The barrier to internal rotation of the acetate methyl group was found to be 93.98 cm-1. Due to the high number of the conformers, a systematic nomenclature will be presented.

  2. Structural and quantum chemical analysis of exciton coupling in homo- and heteroaggregate stacks of merocyanines

    PubMed Central

    Bialas, David; Zitzler-Kunkel, André; Kirchner, Eva; Schmidt, David; Würthner, Frank

    2016-01-01

    Exciton coupling is of fundamental importance and determines functional properties of organic dyes in (opto-)electronic and photovoltaic devices. Here we show that strong exciton coupling is not limited to the situation of equal chromophores as often assumed. Quadruple dye stacks were obtained from two bis(merocyanine) dyes with same or different chromophores, respectively, which dimerize in less-polar solvents resulting in the respective homo- and heteroaggregates. The structures of the quadruple dye stacks were assigned by NMR techniques and unambiguously confirmed by single-crystal X-ray analysis. The heteroaggregate stack formed from the bis(merocyanine) bearing two different chromophores exhibits remarkably different ultraviolet/vis absorption bands compared with those of the homoaggregate of the bis(merocyanine) comprising two identical chromophores. Quantum chemical analysis based on an extension of Kasha's exciton theory appropriately describes the absorption properties of both types of stacks revealing strong exciton coupling also between different chromophores within the heteroaggregate. PMID:27680284

  3. Thermochemistry of dihalogen-substituted benzenes: data evaluation using experimental and quantum chemical methods.

    PubMed

    Verevkin, Sergey P; Emel'yanenko, Vladimir N; Varfolomeev, Mikhail A; Solomonov, Boris N; Zherikova, Kseniya V; Melkhanova, Svetlana V

    2014-12-11

    Temperature dependence of vapor pressures for 12 dihalogen-substituted benzenes (halogen = F, Cl, Br, I) was studied by the transpiration method, and molar vaporization or sublimation enthalpies were derived. These data together with results available in the literature were collected and checked for internal consistency using structure-property correlations. Gas-phase enthalpies of formation of dihalogen-substituted benzenes were calculated by using quantum-chemical methods. Evaluated vaporization enthalpies in combination with gas-phase enthalpies of formation were used for estimation liquid-phase enthalpies of formation of dihalogen-substituted benzenes. Pairwise interactions of halogens on the benzene ring were derived and used for development of simple group additivity procedures for estimation of vaporization enthalpies, gas-phase, and liquid-phase enthalpies of formation of dihalogen-substituted benzenes.

  4. Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform.

    PubMed

    Wu, Xin; Koslowski, Axel; Thiel, Walter

    2012-07-10

    In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

  5. Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

    NASA Technical Reports Server (NTRS)

    Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

    1997-01-01

    The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.

  6. Wavy carbon: A new series of carbon structures explored by quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Ohno, Koichi; Satoh, Hiroko; Iwamoto, Takeaki; Tokoyama, Hiroaki; Yamakado, Hideo

    2015-10-01

    A new carbon family adopting wavy structures has been found by quantum chemical calculations. The key motif of this family is a condensed four-membered ring. Periodically wavy-carbon sheets (wavy-Cn sheets, n = 2, 6, and 8) as well as wavy-C36 tube were found to be very similar to the previously reported prism-Cn carbon tubes (n = 5, 6, and 8) in several respects, including the relative energies per one carbon atom with respect to graphene, CC bond lengths, and CCC bond angles. Because of very high relative energies with respect to graphene (206-253 kJ mol-1), the wavy-carbons may behave as energy reserving materials.

  7. Low temperature regulated growth of PbS quantum dots by wet chemical method

    SciTech Connect

    Kumar, Hitanshu Barman, P. B.; Singh, Ragini Raj; Bind, Umesh Chandra

    2015-08-28

    Narrow size distribution with regulated synthesis of lead sulfide (PbS) quantum dots (QDs) was achieved through wet chemical method. Different concentrations of 2-mercaptoethanol (capping agent) were used for tailoring the QDs size. Transmission electron microscopy and X-ray diffraction studies revealed that the QDs have mean diameters between 6 to 15 nm. The optical absorption spectra were compared to the predictions of a theoretical model for the electronic structure. The theory agrees well with experiment for QDs larger than 7 nm, but for smaller dots there is some deviation from the theoretical predictions. Consequently, the produced particles are having monodispersity, good water solubility, stability and may be good arguments to be biologically compatible due to the use of 2-mercaptoethanol.

  8. Terahertz absorption spectra of oxidized polyethylene and their analysis by quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Komatsu, Marina; Hosobuchi, Masashi; Xie, Xiaojun; Cheng, Yonghong; Furukawa, Yukio; Mizuno, Maya; Fukunaga, Kaori; Ohki, Yoshimichi

    2014-09-01

    Low-density polyethylene, either cross-linked or not, was oxidized and its absorption spectra were measured in the terahertz (THz) range and infrared range. The absorption was increased by the oxidation in the whole THz range. In accord with this, infrared absorption due to carbonyl groups appears. Although these results indicate that the increase in absorption is induced by oxidation, its attribution to resonance or relaxation is unclear. To clarify this point, the vibrational frequencies of three-dimensional polyethylene models with and without carbonyl groups were quantum chemically calculated. As a result, it was clarified that optically inactive skeletal vibrations in polyethylene become active upon oxidation. Furthermore, several absorption peaks due to vibrational resonances are induced by oxidation at wavenumbers from 20 to 100 cm-1. If these absorption peaks are broadened and are superimposed on each other, the absorption spectrum observed experimentally can be reproduced. Therefore, the absorption is ascribable to resonance.

  9. Robust large-gap quantum spin Hall insulators in chemically decorated arsenene films

    NASA Astrophysics Data System (ADS)

    Wang, Dongchao; Chen, Li; Shi, Changmin; Wang, Xiaoli; Cui, Guangliang; Zhang, Pinhua; Chen, Yeqing

    2016-03-01

    Based on first-principles calculations, we propose one new category of two-dimensional topological insulators (2D TIs) in chemically functionalized (-CH3 and -OH) arsenene films. The results show that the surface decorated arsenene (AsCH3 and AsOH) films are intrinsic 2D TIs with sizeable bulk gap. The bulk energy gaps are 0.184 eV, and 0.304 eV in AsCH3 and AsOH films, respectively. Such large bulk gaps make them suitable to realize quantum spin Hall effect in an experimentally accessible temperature regime. Topologically helical edge states in these systems are desirable for dissipationless transport. Moreover, we find that the topological properties in these systems are robust against mechanical deformation by exerting biaxial strain. These novel 2D TIs with large bulk gaps are potential candidate in future electronic devices with ultralow dissipation.

  10. Dissociative electron transfer in polychlorinated aromatics. Reduction potentials from convolution analysis and quantum chemical calculations.

    PubMed

    Romańczyk, Piotr P; Rotko, Grzegorz; Kurek, Stefan S

    2016-08-10

    Formal potentials of the first reduction leading to dechlorination in dimethylformamide were obtained from convolution analysis of voltammetric data and confirmed by quantum chemical calculations for a series of polychlorinated benzenes: hexachlorobenzene (-2.02 V vs. Fc(+)/Fc), pentachloroanisole (-2.14 V), and 2,4-dichlorophenoxy- and 2,4,5-trichlorophenoxyacetic acids (-2.35 V and -2.34 V, respectively). The key parameters required to calculate the reduction potential, electron affinity and/or C-Cl bond dissociation energy, were computed at both DFT-D and CCSD(T)-F12 levels. Comparison of the obtained gas-phase energies and redox potentials with experiment enabled us to verify the relative energetics and the performance of various implicit solvent models. Good agreement with the experiment was achieved for redox potentials computed at the DFT-D level, but only for the stepwise mechanism owing to the error compensation. For the concerted electron transfer/C-Cl bond cleavage process, the application of a high level coupled cluster method is required. Quantum chemical calculations have also demonstrated the significant role of the π*ring and σ*C-Cl orbital mixing. It brings about the stabilisation of the non-planar, C2v-symmetric C6Cl6˙(-) radical anion, explains the experimentally observed low energy barrier and the transfer coefficient close to 0.5 for C6Cl5OCH3 in an electron transfer process followed by immediate C-Cl bond cleavage in solution, and an increase in the probability of dechlorination of di- and trichlorophenoxyacetic acids due to substantial population of the vibrational excited states corresponding to the out-of-plane C-Cl bending at ambient temperatures.

  11. Dissociative electron transfer in polychlorinated aromatics. Reduction potentials from convolution analysis and quantum chemical calculations.

    PubMed

    Romańczyk, Piotr P; Rotko, Grzegorz; Kurek, Stefan S

    2016-08-10

    Formal potentials of the first reduction leading to dechlorination in dimethylformamide were obtained from convolution analysis of voltammetric data and confirmed by quantum chemical calculations for a series of polychlorinated benzenes: hexachlorobenzene (-2.02 V vs. Fc(+)/Fc), pentachloroanisole (-2.14 V), and 2,4-dichlorophenoxy- and 2,4,5-trichlorophenoxyacetic acids (-2.35 V and -2.34 V, respectively). The key parameters required to calculate the reduction potential, electron affinity and/or C-Cl bond dissociation energy, were computed at both DFT-D and CCSD(T)-F12 levels. Comparison of the obtained gas-phase energies and redox potentials with experiment enabled us to verify the relative energetics and the performance of various implicit solvent models. Good agreement with the experiment was achieved for redox potentials computed at the DFT-D level, but only for the stepwise mechanism owing to the error compensation. For the concerted electron transfer/C-Cl bond cleavage process, the application of a high level coupled cluster method is required. Quantum chemical calculations have also demonstrated the significant role of the π*ring and σ*C-Cl orbital mixing. It brings about the stabilisation of the non-planar, C2v-symmetric C6Cl6˙(-) radical anion, explains the experimentally observed low energy barrier and the transfer coefficient close to 0.5 for C6Cl5OCH3 in an electron transfer process followed by immediate C-Cl bond cleavage in solution, and an increase in the probability of dechlorination of di- and trichlorophenoxyacetic acids due to substantial population of the vibrational excited states corresponding to the out-of-plane C-Cl bending at ambient temperatures. PMID:27477334

  12. LDRD final report on high power broadly tunable Mid-IR quantum cascade lasers for improved chemical species detection.

    SciTech Connect

    Wanke, Michael Clement; Hudgens, James J.; Fuller, Charles T.; Samora, Sally; Klem, John Frederick; Young, Erik W.

    2006-01-01

    The goal of our project was to examine a novel quantum cascade laser design that should inherently increase the output power of the laser while simultaneously providing a broad tuning range. Such a laser source enables multiple chemical species identification with a single laser and/or very broad frequency coverage with a small number of different lasers, thus reducing the size and cost of laser based chemical detection systems. In our design concept, the discrete states in quantum cascade lasers are replaced by minibands made of multiple closely spaced electron levels. To facilitate the arduous task of designing miniband-to-miniband quantum cascade lasers, we developed a program that works in conjunction with our existing modeling software to completely automate the design process. Laser designs were grown, characterized, and iterated. The details of the automated design program and the measurement results are summarized in this report.

  13. An enquiry into theoretical bioinorganic chemistry: how heuristic is the character of present-day quantum chemical methods?

    PubMed

    Podewitz, Maren; Stiebritz, Martin T; Reiher, Markus

    2011-01-01

    In this discussion we elaborate on the state of the art in computational bioinorganic chemistry and aim at identifying and defining the most difficult obstacles in the process of obtaining unambiguous and predictive results from quantum chemical calculations. We then proceed to discuss and analyse well-known as well as new concepts for overcoming some of these obstacles.

  14. High-School Students' Conceptual Difficulties and Attempts at Conceptual Change: The Case of Basic Quantum Chemical Concepts

    ERIC Educational Resources Information Center

    Tsaparlis, Georgios; Papaphotis, Georgios

    2009-01-01

    This study tested for deep understanding and critical thinking about basic quantum chemical concepts taught at 12th grade (age 17-18). Our aim was to achieve conceptual change in students. A quantitative study was conducted first (n = 125), and following this 23 selected students took part in semi-structured interviews either individually or in…

  15. Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

    NASA Astrophysics Data System (ADS)

    Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

    2014-05-01

    The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

  16. Use of external cavity quantum cascade laser compliance voltage in real-time trace gas sensing of multiple chemicals

    SciTech Connect

    Phillips, Mark C.; Taubman, Matthew S.; Kriesel, Jason M.

    2015-02-08

    We describe a prototype trace gas sensor designed for real-time detection of multiple chemicals. The sensor uses an external cavity quantum cascade laser (ECQCL) swept over its tuning range of 940-1075 cm-1 (9.30-10.7 µm) at a 10 Hz repetition rate.

  17. Electronic structure evaluation through quantum chemical descriptors of 17β-aminoestrogens with an anticoagulant effect.

    PubMed

    Raya, Angélica; Barrientos-Salcedo, Carolina; Rubio-Póo, Consuelo; Soriano-Correa, Catalina

    2011-06-01

    17β-aminoestrogens have been experimentally studied due to their anticoagulant effect, shown both in in vitro and in vivo assays; this is a non-typical behavior for steroids. The anticoagulant effect of these aminoestrogens has been related to the aromaticity of the A-ring of the steroid molecule; as well as to the length of the amino-alcohol side-chain at C17, which might have an influence on the biological activity of these compounds. The study of the electronic structure of 17β-aminoestrogens using quantum chemical descriptors could provide significant information and may contribute to a better understanding of structure-activity relationships in these molecules. In this work, we present a density functional theory (DFT) study at the B3LYP level of theory for selected 17β-aminoestrogens compounds, with the main purpose of characterizing their electronic and physicochemical properties and relating them to their anticoagulant effect, using quantum chemical descriptors such as: atomic charges, bond order, electrostatic potential isosurface analysis, hardness, electrophilicity and aromaticity indexes. The results obtained from these quantum chemical descriptors, led us to characterize the physicochemical properties, reactive sites and substituent influence on electronic structure, as well as to identify additional quantum chemical descriptors that could be associated with the anticoagulant effect of 17β-aminoestrogens.

  18. Chemical Potential for the Interacting Classical Gas and the Ideal Quantum Gas Obeying a Generalized Exclusion Principle

    ERIC Educational Resources Information Center

    Sevilla, F. J.; Olivares-Quiroz, L.

    2012-01-01

    In this work, we address the concept of the chemical potential [mu] in classical and quantum gases towards the calculation of the equation of state [mu] = [mu](n, T) where n is the particle density and "T" the absolute temperature using the methods of equilibrium statistical mechanics. Two cases seldom discussed in elementary textbooks are…

  19. Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis.

    PubMed

    Mobli, Mehdi; Abraham, Raymond J

    2005-03-01

    A model based on classical concepts is derived to describe the effect of the nitro group on proton chemical shifts. The calculated chemical shifts are then compared to ab initio (GIAO) calculated chemical shifts. The accuracy of the two models is assessed using proton chemical shifts of a set of rigid organic nitro compounds that are fully assigned in CDCl3 at 700 MHz. The two methods are then used to evaluate the accuracy of different popular post-SCF methods (B3LYP and MP2) and molecular mechanics methods (MMX and MMFF94) in calculating the molecular structure of a set of sterically crowded nitro aromatic compounds. Both models perform well on the rigid molecules used as a test set, although when using the GIAO method a general overestimation of the deshielding of protons near the nitro group is observed. The analysis of the sterically crowded molecules shows that the very popular B3LYP/6-31G(d,p) method produces very poor twist angles for these, and that using a larger basis set [6-311++G(2d,p)] gives much more reasonable results. The MP2 calculations, on the other hand, overestimate the twist angles, which for these compounds compensates for the deshielding effect generally observed for protons near electronegative atoms when using the GIAO method at the B3LYP/6-311++G(2d,p) level. The most accurate results are found when the structures are calculated using B3LYP/6-311++G(2d,p) level of theory, and the chemical shifts are calculated using the CHARGE program based on classical models.

  20. Quantum-chemical study of interactions of trans-resveratrol with guanine-thymine dinucleotide and DNA-nucleobases.

    PubMed

    Mikulski, Damian; Szeląg, Małgorzata; Molski, Marcin

    2011-12-01

    Trans-resveratrol, a natural phytoalexin present in red wine and grapes, has gained considerable attention because of its antiproliferative, chemopreventive and proapoptotic activity against human cancer cells. The accurate quantum-chemical computations based on the density functional theory (DFT) and ab initio second-order Møller-Plesset perturbation method (MP2) have been performed for the first time to study interactions of trans-resveratrol with guanine-thymine dinucleotide and DNA-derived nitrogenous bases: adenine, guanine, cytosine and thymine in vacuum and water medium. This compound is found to show high affinity to nitrogenous bases and guanine-thymine dinucleotide. The electrostatic interactions from intermolecular hydrogen bonding increase the stability of complexes studied. In particular, significantly strong hydrogen bonds between 4'-H atom of trans-resveratrol and imidazole nitrogen as well as carbonyl oxygen atoms of nucleobases studied stabilize these systems. The stabilization energies computed reveal that the negatively charged trans-resveratrol-dinucleotide complex is more energetically stable in water medium than in vacuum. MP2 method gives more reliable and significantly high values of stabilization energy of trans-resveratrol-dinucleotide, trans-resveratrol-guanine and trans-resveratrol-thymine complexes than B3LYP exchange-correlation functional because it takes into account London dispersion energy. According to the results, in the presence of trans-resveratrol the 3'-5' phosphodiester bond in dinucleotide can be cleaved and the proton from 4'-OH group of trans-resveratrol migrates to the 3'-O atom of dinucleotide. It is concluded that trans-resveratrol is able to break the DNA strand. Hence, the findings obtained help understand antiproliferative and anticancer properties of this polyphenol.

  1. Biochemical characterization of the castor bean ent-kaurene synthase(-like) family supports quantum chemical view of diterpene cyclization.

    PubMed

    Jackson, Alana J; Hershey, David M; Chesnut, Taylor; Xu, Meimei; Peters, Reuben J

    2014-07-01

    It has become apparent that plants have extensively diversified their arsenal of labdane-related diterpenoids (LRDs), in part via gene duplication and neo-functionalization of the ancestral ent-kaurene synthase (KS) required for gibberellin metabolism. For example, castor bean (Ricinus communis) was previously shown to produce an interesting set of biosynthetically related diterpenes, specifically ent-sandracopimaradiene, ent-beyerene, and ent-trachylobane, in addition to ent-kaurene, using four separate diterpene synthases, albeit these remain unidentified. Notably, despite mechanistic similarity of the underlying reaction to that catalyzed by KSs, ent-beyerene and ent-trachylobane synthases have not yet been identified. Given our interest in LRD biosynthesis, and the recent availability of the castor bean genome sequence, a synthetic biology approach was applied to biochemically characterize the four KS(-like) enzymes [KS(L)s] found in Ricinus communis [i.e., the RcKS(L)s]. In particular, using bacteria engineered to produce the relevant ent-copalyl diphosphate precursor and synthetic genes based on the predicted RcKS(L)s, although this ultimately required correction of a "splicing" error in one of the predicted genes, highlighting the dependence of such a synthetic biology approach on accurate gene sequences. Nevertheless, it is possible to assign each of the four RcKS(L)s to one of the previously observed diterpene synthase activities, providing access to functionally enzymes. Intriguingly, the product distribution of the RcKS(L)s seems to support the distinct diterpene synthase reaction mechanism proposed by quantum chemical calculations, rather than the classically proposed pathway.

  2. Biochemical characterization of the castor bean ent-kaurene synthase(-like) family supports quantum chemical view of diterpene cyclization

    PubMed Central

    Jackson, Alana J.; Hershey, David M.; Chesnut, Taylor; Xu, Meimei; Peters, Reuben J.

    2014-01-01

    It has become apparent that plants have extensively diversified their arsenal of labdane-related diterpenoids (LRDs), in part via gene duplication and neo-functionalization of the ancestral ent-kaurene synthase (KS) required for gibberellin metabolism. For example, castor bean (Ricinus communis) was previously shown to produce an interesting set of biosynthetically related diterpenes, specifically ent-sandracopimaradiene, ent-beyerene, and ent-trachylobane, in addition to ent-kaurene, using four separate diterpene synthases, albeit these remain unidentified. Notably, despite mechanistic similarity of the underlying reaction to that catalyzed by KSs, ent-beyerene and ent-trachylobane synthases have not yet been identified. Given our interest in LRD biosynthesis, and the recent availability of the castor bean genome sequence, we applied a synthetic biology approach to biochemically characterize the four KS(-like) enzymes [KS(L)s] found in Ricinus communis [i.e., the RcKS(L)s]. In particular, using bacteria engineered to produce the relevant ent-copalyl diphosphate precursor and synthetic genes based on the predicted RcKS(L)s, although this ultimately required correction of a “splicing” error in one of the predicted genes, highlighting the dependence of such a synthetic biology approach on accurate gene sequences. Nevertheless, we can assign each of the four RcKS(L)s to one of the previously observed diterpene synthase activities, providing access to functionally novel enzymes. Intriguingly, the product distribution of the RcKS(L)s seems to support the distinct diterpene synthase reaction mechanism proposed by quantum chemical calculations, rather than the classically proposed pathway. PMID:24810014

  3. Quantum chemical study on the stability of honeybee queen pheromone against atmospheric factors.

    PubMed

    Shi, Rongwei; Liu, Fanglin

    2016-06-01

    The managed honeybee, Apis mellifera, has been experienced a puzzling event, termed as colony collapse disorder (CCD), in which worker bees abruptly disappear from their hives. Potential factors include parasites, pesticides, malnutrition, and environmental stresses. However, so far, no definitive relationship has been established between specific causal factors and CCD events. Here we theoretically test whether atmospheric environment could disturb the chemical communication between the queen and their workers in a colony. A quantum chemistry method has been used to investigate for the stability of the component of A. mellifera queen mandibular pheromone (QMP), (E)-9-keto-2-decenoic acid (9-ODA), against atmospheric water and free radicals. The results show that 9-ODA is less likely to react with water due to the high barrier heights (~36.5 kcal · mol(-1)) and very low reaction rates. However, it can easily react with triplet oxygen and hydroxyl radicals because of low or negative energy barriers. Thus, the atmospheric free radicals may disturb the chemical communication between the queen and their daughters in a colony. Our pilot study provides new insight for the cause of CCD, which has been reported throughout the world. PMID:27207255

  4. Portable open-path chemical sensor using a quantum cascade laser

    NASA Astrophysics Data System (ADS)

    Corrigan, Paul; Lwin, Maung; Huntley, Reuven; Chhabra, Amandeep; Moshary, Fred; Gross, Barry; Ahmed, Samir

    2009-05-01

    Remote sensing of enemy installations or their movements by trace gas detection is a critical but challenging military objective. Open path measurements over ranges of a few meters to many kilometers with sensitivity in the parts per million or billion regime are crucial in anticipating the presence of a threat. Previous approaches to detect ground level chemical plumes, explosive constituents, or combustion have relied on low-resolution, short range Fourier transform infrared spectrometer (FTIR), or low-sensitivity near-infrared differential optical absorption spectroscopy (DOAS). As mid-infrared quantum cascade laser (QCL) sources have improved in cost and performance, systems based on QCL's that can be tailored to monitor multiple chemical species in real time are becoming a viable alternative. We present the design of a portable, high-resolution, multi-kilometer open path trace gas sensor based on QCL technology. Using a tunable (1045-1047cm-1) QCL, a modeled atmosphere and link-budget analysis with commercial component specifications, we show that with this approach, accuracy in parts per billion ozone or ammonia can be obtained in seconds at path lengths up to 10 km. We have assembled an open-path QCL sensor based on this theoretical approach at City College of New York, and we present preliminary results demonstrating the potential of QCLs in open-path sensing applications.

  5. Synthesis, vibrational and quantum chemical investigations of hydrogen bonded complex betaine dihydrogen selenite

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Marchewka, Mariusz K.; Kalaivani, M.

    2012-10-01

    The molecular complex of betaine with selenious acid namely, betaine dihydrogen selenite (C5H13NO5Se, BDHSe) was synthesised by the reaction of betaine and SeO2 in a 1:1:1 solution of isopropanol, methanol and water. Crystals were grown from this solution by cooling to 253 K for few days. The complex was formed without accompanying proton transfer from selenious acid molecule to betaine. The complete vibrational assignments and analysis of BDHSe have been performed by FTIR, FT-Raman and far-infrared spectral studies. More support on the experimental findings was added from the quantum chemical studies performed with DFT (B3LYP) method using 6-311++G∗∗, 6-31G∗∗, cc-pVDZ and 3-21G basis sets. The structural parameters, energies, thermodynamic parameters and the NBO charges of BDHSe were determined by the DFT method. The 1H and 13C isotropic chemical shifts (δ ppm) of BDHSe with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. SHG experiment was carried out using Kurtz-Perry powder technique. The efficiency of second harmonic generation for BDHSe was estimated relatively to KDP: deff = 0.97 deff (KDP).

  6. Quantum chemical study on the stability of honeybee queen pheromone against atmospheric factors.

    PubMed

    Shi, Rongwei; Liu, Fanglin

    2016-06-01

    The managed honeybee, Apis mellifera, has been experienced a puzzling event, termed as colony collapse disorder (CCD), in which worker bees abruptly disappear from their hives. Potential factors include parasites, pesticides, malnutrition, and environmental stresses. However, so far, no definitive relationship has been established between specific causal factors and CCD events. Here we theoretically test whether atmospheric environment could disturb the chemical communication between the queen and their workers in a colony. A quantum chemistry method has been used to investigate for the stability of the component of A. mellifera queen mandibular pheromone (QMP), (E)-9-keto-2-decenoic acid (9-ODA), against atmospheric water and free radicals. The results show that 9-ODA is less likely to react with water due to the high barrier heights (~36.5 kcal · mol(-1)) and very low reaction rates. However, it can easily react with triplet oxygen and hydroxyl radicals because of low or negative energy barriers. Thus, the atmospheric free radicals may disturb the chemical communication between the queen and their daughters in a colony. Our pilot study provides new insight for the cause of CCD, which has been reported throughout the world.

  7. Atomistic-level non-equilibrium model for chemically reactive systems based on steepest-entropy-ascent quantum thermodynamics

    NASA Astrophysics Data System (ADS)

    Li, Guanchen; Al-Abbasi, Omar; von Spakovsky, Michael R.

    2014-10-01

    This paper outlines an atomistic-level framework for modeling the non-equilibrium behavior of chemically reactive systems. The framework called steepest- entropy-ascent quantum thermodynamics (SEA-QT) is based on the paradigm of intrinsic quantum thermodynamic (IQT), which is a theory that unifies quantum mechanics and thermodynamics into a single discipline with wide applications to the study of non-equilibrium phenomena at the atomistic level. SEA-QT is a novel approach for describing the state of chemically reactive systems as well as the kinetic and dynamic features of the reaction process without any assumptions of near-equilibrium states or weak-interactions with a reservoir or bath. Entropy generation is the basis of the dissipation which takes place internal to the system and is, thus, the driving force of the chemical reaction(s). The SEA-QT non-equilibrium model is able to provide detailed information during the reaction process, providing a picture of the changes occurring in key thermodynamic properties (e.g., the instantaneous species concentrations, entropy and entropy generation, reaction coordinate, chemical affinities, reaction rate, etc). As an illustration, the SEA-QT framework is applied to an atomistic-level chemically reactive system governed by the reaction mechanism F + H2 leftrightarrow FH + H.

  8. Techniques for Accurate Sizing of Gold Nanoparticles Using Dynamic Light Scattering with Particular Application to Chemical and Biological Sensing Based on Aggregate Formation.

    PubMed

    Zheng, Tianyu; Bott, Steven; Huo, Qun

    2016-08-24

    Gold nanoparticles (AuNPs) have found broad applications in chemical and biological sensing, catalysis, biomolecular imaging, in vitro diagnostics, cancer therapy, and many other areas. Dynamic light scattering (DLS) is an analytical tool used routinely for nanoparticle size measurement and analysis. Due to its relatively low cost and ease of operation in comparison to other more sophisticated techniques, DLS is the primary choice of instrumentation for analyzing the size and size distribution of nanoparticle suspensions. However, many DLS users are unfamiliar with the principles behind the DLS measurement and are unware of some of the intrinsic limitations as well as the unique capabilities of this technique. The lack of sufficient understanding of DLS often leads to inappropriate experimental design and misinterpretation of the data. In this study, we performed DLS analyses on a series of citrate-stabilized AuNPs with diameters ranging from 10 to 100 nm. Our study shows that the measured hydrodynamic diameters of the AuNPs can vary significantly with concentration and incident laser power. The scattered light intensity of the AuNPs has a nearly sixth order power law increase with diameter, and the enormous scattered light intensity of AuNPs with diameters around or exceeding 80 nm causes a substantial multiple scattering effect in conventional DLS instruments. The effect leads to significant errors in the reported average hydrodynamic diameter of the AuNPs when the measurements are analyzed in the conventional way, without accounting for the multiple scattering. We present here some useful methods to obtain the accurate hydrodynamic size of the AuNPs using DLS. We also demonstrate and explain an extremely powerful aspect of DLS-its exceptional sensitivity in detecting gold nanoparticle aggregate formation, and the use of this unique capability for chemical and biological sensing applications. PMID:27472008

  9. Quantum Chemical Study of Raman Spectroscopy of Substituted Benzene Derivatives Adsorbed on Metal Surfaces

    NASA Astrophysics Data System (ADS)

    Wu, De-Yin; Tian, Zhong-Qun

    2011-06-01

    Surface-enhanced Raman spectroscopy (SERS) can be applied to obtain the information of molecules at the noble metal surfaces. But there are a number of difficulties to clearly correlate Raman spectra with microscopic molecular structures on metal surfaces. The main reason is that it is difficult to characterize unambiguously the metal surface structures and the influence of the binding interaction on SERS signals of the probe molecules. According to the surface selection rule of SERS, the electromagnetic enhancement will not change relative Raman intensities of vibrational modes with the same irreducible representation. Therefore, the change of the relative Raman intensities of the total symmetric modes may only originate from the chemical enhancement. In order to understand how the chemical interaction modulates the Raman intensity of individual modes, it is necessary to systematically investigate the Raman spectra of probe molecules themselves and the dependence of SERS signals on the binding interaction, adsorption sites, excitation wavelengths and metal property. Some probe molecules, including aniline, 1,4-benzenediamine, p-aminothiophenol, benzyl chlorine, and 4,4^'-bipyridine are investigated based on quantum chemical calculations. Raman spectra of these molecules and their adsorbed species were predicted and compared with experimentally measured spectra. The metal surfaces were mimicked using the metallic cluster model, where the silver or gold surfaces were replaced by silver or gold clusters, respectively. The density functional theory approach was employed to obtain the optimized structures and vibrational spectra by combining all-electron basis sets of 6-311+G** for atoms in the molecules and the poseudopotential basis set of LANL2DZ for metal atoms. The vibrational frequency shift and the relative Raman intensity are related to the adsorption configuration of the probe molecules. For all these molecules, the ring breathing mode and the C-C stretching

  10. Quantum chemical topology (QCT) descriptors as substitutes for appropriate Hammett constants.

    PubMed

    Smith, P J; Popelier, P L A

    2005-09-21

    A technique called quantum topological molecular similarity (QTMS) was recently proposed [J. Chem. Inf. Comput. Sci., 2001, 41, 764] in order to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs, based on modern ab initio wave functions of geometry optimised molecules, in combination with quantum chemical topology (QCT). The current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In previous work [J. Chem. Soc., Perkin Trans. 2, 2002, 1231] it was proven that a set of Hammett constants (sigma(p), sigma(m), sigma(I) and sigma(p)0) for a sizeable set of mono- and polysubstituted carboxylic acids can be replaced by QCT bond descriptors. Using QTMS and proper statistical validation we examined seven data sets in total. The first three sets (para-substituted phenols (sigma-), substituted toluenes (sigma+) and bromophenethylamines (sigma+)) corroborate that a wider class of Hammett constants can also be replaced by QCT descriptors. A fourth set (benzyl radicals) focuses on non-Hammett behaviour being superimposed on Hammett behaviour. QCT descriptors selectively correlate with Hammett behaviour. The QTMS analysis of the last three sets (toxicity of benzyl alcohols, chromatographic capacity factors of chalcones and herbicidal activity of 5-chloro-2,3-dicyanopyrazines) screens for false positives. This test is successfully passed in that QCT descriptors fail when lipophilicity/hydrophobicity is in charge. Hence, overall, the discriminatory capacity of QCT descriptors is established, in detecting Hammett behaviour and specifically replacing the Hammett constants by more modern and non-empirical descriptors.

  11. CRITIC2: A program for real-space analysis of quantum chemical interactions in solids

    NASA Astrophysics Data System (ADS)

    Otero-de-la-Roza, A.; Johnson, Erin R.; Luaña, Víctor

    2014-03-01

    We present CRITIC2, a program for the analysis of quantum-mechanical atomic and molecular interactions in periodic solids. This code, a greatly improved version of the previous CRITIC program (Otero-de-la Roza et al., 2009), can: (i) find critical points of the electron density and related scalar fields such as the electron localization function (ELF), Laplacian, … (ii) integrate atomic properties in the framework of Bader’s Atoms-in-Molecules theory (QTAIM), (iii) visualize non-covalent interactions in crystals using the non-covalent interactions (NCI) index, (iv) generate relevant graphical representations including lines, planes, gradient paths, contour plots, atomic basins, … and (v) perform transformations between file formats describing scalar fields and crystal structures. CRITIC2 can interface with the output produced by a variety of electronic structure programs including WIEN2k, elk, PI, abinit, Quantum ESPRESSO, VASP, Gaussian, and, in general, any other code capable of writing the scalar field under study to a three-dimensional grid. CRITIC2 is parallelized, completely documented (including illustrative test cases) and publicly available under the GNU General Public License. Catalogue identifier: AECB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 11686949 No. of bytes in distributed program, including test data, etc.: 337020731 Distribution format: tar.gz Programming language: Fortran 77 and 90. Computer: Workstations. Operating system: Unix, GNU/Linux. Has the code been vectorized or parallelized?: Shared-memory parallelization can be used for most tasks. Classification: 7.3. Catalogue identifier of previous version: AECB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 157 Nature of problem: Analysis of quantum-chemical

  12. The electrochemistry of transparent quantum size rutile nanowire thin films prepared by one-step low temperature chemical bath deposition

    NASA Astrophysics Data System (ADS)

    Berger, Thomas; Lana-Villarreal, Teresa; Monllor-Satoca, Damián; Gómez, Roberto

    2007-10-01

    We performed a spectro- and photoelectrochemical study of electrodes consisting of oriented rutile TiO 2 nanowires with a diameter of ˜2 nm prepared directly by chemical bath deposition on conducting glass. A significant increase (around 0.25 eV with respect to bulk rutile) of the band gap energy for the nanowire film is observed and attributed to quantum size effects, pointing to the presence of individual monocrystalline nanowires with no significant electronic communication among them. This allows for the investigation of morphologically well defined electrodes in the two dimensional quantum confinement regime, which are characterized by particularly good photoelectrocatalytic and electrochromic properties.

  13. Adaptive Neuro-Fuzzy Inference System Applied QSAR with Quantum Chemical Descriptors for Predicting Radical Scavenging Activities of Carotenoids.

    PubMed

    Jhin, Changho; Hwang, Keum Taek

    2015-01-01

    One of the physiological characteristics of carotenoids is their radical scavenging activity. In this study, the relationship between radical scavenging activities and quantum chemical descriptors of carotenoids was determined. Adaptive neuro-fuzzy inference system (ANFIS) applied quantitative structure-activity relationship models (QSAR) were also developed for predicting and comparing radical scavenging activities of carotenoids. Semi-empirical PM6 and PM7 quantum chemical calculations were done by MOPAC. Ionisation energies of neutral and monovalent cationic carotenoids and the product of chemical potentials of neutral and monovalent cationic carotenoids were significantly correlated with the radical scavenging activities, and consequently these descriptors were used as independent variables for the QSAR study. The ANFIS applied QSAR models were developed with two triangular-shaped input membership functions made for each of the independent variables and optimised by a backpropagation method. High prediction efficiencies were achieved by the ANFIS applied QSAR. The R-square values of the developed QSAR models with the variables calculated by PM6 and PM7 methods were 0.921 and 0.902, respectively. The results of this study demonstrated reliabilities of the selected quantum chemical descriptors and the significance of QSAR models. PMID:26474167

  14. Adaptive Neuro-Fuzzy Inference System Applied QSAR with Quantum Chemical Descriptors for Predicting Radical Scavenging Activities of Carotenoids

    PubMed Central

    Jhin, Changho; Hwang, Keum Taek

    2015-01-01

    One of the physiological characteristics of carotenoids is their radical scavenging activity. In this study, the relationship between radical scavenging activities and quantum chemical descriptors of carotenoids was determined. Adaptive neuro-fuzzy inference system (ANFIS) applied quantitative structure-activity relationship models (QSAR) were also developed for predicting and comparing radical scavenging activities of carotenoids. Semi-empirical PM6 and PM7 quantum chemical calculations were done by MOPAC. Ionisation energies of neutral and monovalent cationic carotenoids and the product of chemical potentials of neutral and monovalent cationic carotenoids were significantly correlated with the radical scavenging activities, and consequently these descriptors were used as independent variables for the QSAR study. The ANFIS applied QSAR models were developed with two triangular-shaped input membership functions made for each of the independent variables and optimised by a backpropagation method. High prediction efficiencies were achieved by the ANFIS applied QSAR. The R-square values of the developed QSAR models with the variables calculated by PM6 and PM7 methods were 0.921 and 0.902, respectively. The results of this study demonstrated reliabilities of the selected quantum chemical descriptors and the significance of QSAR models. PMID:26474167

  15. The hydrogen peroxide-rare gas systems: quantum chemical calculations and hyperspherical harmonic representation of the potential energy surface for atom-floppy molecule interactions.

    PubMed

    Barreto, Patricia R P; Vilela, Alessandra F A; Lombardi, Andrea; Maciel, Glauciete S; Palazzetti, Federico; Aquilanti, Vincenzo

    2007-12-13

    A quantum chemical exploration is reported on the interaction potentials of H2O2 with the rare gases, He, Ne, Ar, Kr, and Xe. Hydrogen peroxide (the simplest example of chiral molecule in its equilibrium geometry) is modeled as rigid except for the torsional mode around the O-O bond. However, on the basis of previous work (Maciel, G. S.; et al. Chem. Phys. Lett. 2006 432, 383), the internal mode description is based, rather than on the vectors of the usual valence picture, on the orthogonal local representation, which was demonstrated useful for molecular dynamics simulations, because the torsion around the vector joining the center-of-mass of the two OH radicals mimics accurately the adiabatic reaction path for chirality changing isomerization, following the torsional potential energy profile from equilibrium through the barriers for the trans and cis geometries. The basic motivation of this work is the determination of potential energy surfaces for the interactions to be used in classical and quantum simulations of molecular collisions, specifically those leading to chirality changes of possible relevance in the modeling of prebiotic phenomena. Particular attention is devoted to the definition of coordinates and expansion formulas for the potentials, allowing for a faithful representation of geometrical and symmetry properties of these systems, prototypical of the interaction of an atom with a floppy molecule.

  16. Fully Coriolis-coupled quantum studies of the H + O2 (upsilon i = 0-2, j i = 0,1) --> OH + O reaction on an accurate potential energy surface: integral cross sections and rate constants.

    PubMed

    Lin, Shi Ying; Sun, Zhigang; Guo, Hua; Zhang, Dong Hui; Honvault, Pascal; Xie, Daiqian; Lee, Soo-Y

    2008-01-31

    We present accurate quantum calculations of the integral cross section and rate constant for the H + O2 --> OH + O combustion reaction on a recently developed ab initio potential energy surface using parallelized time-dependent and Chebyshev wavepacket methods. Partial wave contributions up to J = 70 were computed with full Coriolis coupling, which enabled us to obtain the initial state-specified integral cross sections up to 2.0 eV of the collision energy and thermal rate constants up to 3000 K. The integral cross sections show a large reaction threshold due to the quantum endothermicity of the reaction, and they monotonically increase with the collision energy. As a result, the temperature dependence of the rate constant is of the Arrhenius type. In addition, it was found that reactivity is enhanced by reactant vibrational excitation. The calculated thermal rate constant shows a significant improvement over that obtained on the DMBE IV potential, but it still underestimates the experimental consensus.

  17. Quantum chemical and experimental studies on polymorphism of antiviral drug Lamivudine

    NASA Astrophysics Data System (ADS)

    Ramkumaar, G. R.; Srinivasan, S.; Bhoopathy, T. J.; Gunasekaran, S.

    2012-12-01

    Lamivudine, is chemically known as [4-amino-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]-1,2-dihydropyrimidin-2-one], is an anti-HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. Spectral characteristics of Lamivudine have been studied by methods of FTIR, NMR and quantum chemistry. The FTIR and spectra of Lamivudine was recorded in the regions 4000-400 cm-1. The thermal stability of Lamivudine was studied by the thermogravimetric analysis (TGA). The isotropic 13C-nuclear magnetic shielding constants of this compound were calculated by employing the direct implementation of the gauge including-atomic-orbital (GIAO) method at the HF and B3LYP density functional theory using 6-31G(d,p) basis set. The optimized molecular geometry, bond orders, harmonic vibrational spectrum of anhydrous and hydrated Lamivudine were calculated by restricted Hartree Fock and density functional B3LYP method with the 6-31G(d,p) basis set using Gaussian 03W program.

  18. Structural studies on ethyl isovalerate by microwave spectroscopy and quantum chemical calculations.

    PubMed

    Mouhib, Halima; Jelisavac, Dragan; Sutikdja, Lilian W; Isaak, Elisabeth; Stahl, Wolfgang

    2011-01-20

    We observed the microwave spectrum of ethyl isovalerate by molecular beam Fourier transform microwave spectroscopy. The rotational and centrifugal distortion constants of the most abundant conformer were determined. Its structure was investigated by comparison of the experimental rotational constants with those obtained by ab initio methods. In a first step, the rotational constants of various conformers were calculated at the MP2/6-311++G** level of theory. Surprisingly, no agreement with the experimental results was found. Therefore, we concluded that in the case of ethyl isovalerate more advanced quantum chemical methods are required to obtain a reliable molecular geometry. Ab initio calculations carried out at MP3/6-311++G**, MP4/6-311++G**, and CCSD/6-311++G** levels and also density functional theory calculations using the B3LYP/6-311++G** method gave similar results for the rotational constants, but they were clearly distinct from those obtained at the MP2/6-311++G** level. With use of these more advanced methods, the rotational constants of the lowest energy conformer were in good agreement with those obtained from the microwave spectrum.

  19. Silicon Oxysulfide, OSiS: Rotational Spectrum, Quantum-Chemical Calculations, and Equilibrium Structure.

    PubMed

    Thorwirth, Sven; Mück, Leonie Anna; Gauss, Jürgen; Tamassia, Filippo; Lattanzi, Valerio; McCarthy, Michael C

    2011-06-01

    Silicon oxysulfide, OSiS, and seven of its minor isotopic species have been characterized for the first time in the gas phase at high spectral resolution by means of Fourier transform microwave spectroscopy. The equilibrium structure of OSiS has been determined from the experimental data using calculated vibration-rotation interaction constants. The structural parameters (rO-Si = 1.5064 Å and rSi-S = 1.9133 Å) are in very good agreement with values from high-level quantum chemical calculations using coupled-cluster techniques together with sophisticated additivity and extrapolation schemes. The bond distances in OSiS are very short in comparison with those in SiO and SiS. This unexpected finding is explained by the partial charges calculated for OSiS via a natural population analysis. The results suggest that electrostatic effects rather than multiple bonding are the key factors in determining bonding in this triatomic molecule. The data presented provide the spectroscopic information needed for radio astronomical searches for OSiS.

  20. Octafluorodirhenate(III) Revisited: Solid-State Preparation, Characterization, and Multiconfigurational Quantum Chemical Calculations.

    PubMed

    Mariappan Balasekaran, Samundeeswari; Todorova, Tanya K; Pham, Chien Thang; Hartmann, Thomas; Abram, Ulrich; Sattelberger, Alfred P; Poineau, Frederic

    2016-06-01

    A simple method for the high-yield preparation of (NH4)2[Re2F8]·2H2O has been developed that involves the reaction of (n-Bu4N)2[Re2Cl8] with molten ammonium bifluoride (NH4HF2). Using this method, the new salt [NH4]2[Re2F8]·2H2O was prepared in ∼90% yield. The product was characterized in solution by ultraviolet-visible light (UV-vis) and (19)F nuclear magnetic resonance ((19)F NMR) spectroscopies and in the solid-state by elemental analysis, powder X-ray diffraction (XRD), and infrared (IR) spectroscopy. Multiconfigurational CASSCF/CASPT2 quantum chemical calculations were performed to investigate the molecular and electronic structure, as well as the electronic absorption spectrum of the [Re2F8](2-) anion. The metal-metal bonding in the Re2(6+) unit was quantified in terms of effective bond order (EBO) and compared to that of its [Re2Cl8](2-) and [Re2Br8](2-) analogues.

  1. Quantum Monte Carlo for large chemical systems: implementing efficient strategies for petascale platforms and beyond.

    PubMed

    Scemama, Anthony; Caffarel, Michel; Oseret, Emmanuel; Jalby, William

    2013-04-30

    Various strategies to implement efficiently quantum Monte Carlo (QMC) simulations for large chemical systems are presented. These include: (i) the introduction of an efficient algorithm to calculate the computationally expensive Slater matrices. This novel scheme is based on the use of the highly localized character of atomic Gaussian basis functions (not the molecular orbitals as usually done), (ii) the possibility of keeping the memory footprint minimal, (iii) the important enhancement of single-core performance when efficient optimization tools are used, and (iv) the definition of a universal, dynamic, fault-tolerant, and load-balanced framework adapted to all kinds of computational platforms (massively parallel machines, clusters, or distributed grids). These strategies have been implemented in the QMC=Chem code developed at Toulouse and illustrated with numerical applications on small peptides of increasing sizes (158, 434, 1056, and 1731 electrons). Using 10-80 k computing cores of the Curie machine (GENCI-TGCC-CEA, France), QMC=Chem has been shown to be capable of running at the petascale level, thus demonstrating that for this machine a large part of the peak performance can be achieved. Implementation of large-scale QMC simulations for future exascale platforms with a comparable level of efficiency is expected to be feasible.

  2. Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid-Corlumine

    NASA Astrophysics Data System (ADS)

    Mishra, Rashmi; Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2014-01-01

    The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

  3. The vibration properties of the (n,0) boron nitride nanotubes from ab initio quantum chemical simulations

    NASA Astrophysics Data System (ADS)

    Erba, A.; Ferrabone, M.; Baima, J.; Orlando, R.; Rérat, M.; Dovesi, R.

    2013-02-01

    The vibration spectrum of single-walled zigzag boron nitride (BN) nanotubes is simulated with an ab initio periodic quantum chemical method. The trend towards the hexagonal monolayer (h-BN) in the limit of large tube radius R is explored for a variety of properties related to the vibrational spectrum: vibration frequencies, infrared intensities, oscillator strengths, and vibration contributions to the polarizability tensor. The (n,0) family is investigated in the range from n = 6 (24 atoms in the unit cell and tube radius R = 2.5 Å) to n = 60 (240 atoms in the cell and R = 24.0 Å). Simulations are performed using the CRYSTAL program which fully exploits the rich symmetry of this class of one-dimensional periodic systems: 4n symmetry operators for the general (n,0) tube. Three sets of infrared active phonon bands are found in the spectrum. The first one lies in the 0-600 cm-1 range and goes regularly to zero when R increases; the connection between these normal modes and the elastic and piezoelectric constants of h-BN is discussed. The second (600-800 cm-1) and third (1300-1600 cm-1) sets tend regularly, but with quite different speed, to the optical modes of the h-BN layer. The vibrational contribution of these modes to the two components (parallel and perpendicular) of the polarizability tensor is also discussed.

  4. Interactions of ionic liquids and acetone: thermodynamic properties, quantum-chemical calculations, and NMR analysis.

    PubMed

    Ruiz, Elia; Ferro, Victor R; Palomar, Jose; Ortega, Juan; Rodriguez, Juan Jose

    2013-06-20

    The interactions between ionic liquids (ILs) and acetone have been studied to obtain a further understanding of the behavior of their mixtures, which generally give place to an exothermic process, mutual miscibility, and negative deviation of Raoult's law. COSMO-RS was used as a suitable computational method to systematically analyze the excess enthalpy of IL-acetone systems (>300), in terms of the intermolecular interactions contributing to the mixture behavior. Spectroscopic and COSMO-RS results indicated that acetone, as a polar compound with strong hydrogen bond acceptor character, in most cases, establishes favorable hydrogen bonding with ILs. This interaction is strengthened by the presence of an acidic cation and an anion with dispersed charge and non-HB acceptor character in the IL. COSMO-RS predictions indicated that gas-liquid and vapor-liquid equilibrium data for IL-acetone systems can be finely tuned by the IL selection, that is, acting on the intermolecular interactions between the molecular and ionic species in the liquid phase. NMR measurements for IL-acetone mixtures at different concentrations were also carried out. Quantum-chemical calculations by using molecular clusters of acetone and IL species were finally performed. These results provided additional evidence of the main role played by hydrogen bonding in the behavior of systems containing ILs and HB acceptor compounds, such as acetone. PMID:23688030

  5. Uranium and thorium hydride complexes as multielectron reductants: a combined neutron diffraction and quantum chemical study.

    PubMed

    Grant, Daniel J; Stewart, Timothy J; Bau, Robert; Miller, Kevin A; Mason, Sax A; Gutmann, Matthias; McIntyre, Garry J; Gagliardi, Laura; Evans, William J

    2012-03-19

    The unusual uranium reaction system in which uranium(4+) and uranium(3+) hydrides interconvert by formal bimetallic reductive elimination and oxidative addition reactions, [(C(5)Me(5))(2)UH(2)](2) (1) ⇌ [(C(5)Me(5))(2)UH](2) (2) + H(2), was studied by employing multiconfigurational quantum chemical and density functional theory methods. 1 can act as a formal four-electron reductant, releasing H(2) gas as the byproduct of four H(2)/H(-) redox couples. The calculated structures for both reactants and products are in good agreement with the X-ray diffraction data on 2 and 1 and the neutron diffraction data on 1 obtained under H(2) pressure as part of this study. The interconversion of the uranium(4+) and uranium(3+) hydride species was calculated to be near thermoneutral (~-2 kcal/mol). Comparison with the unknown thorium analogue, [(C(5)Me(5))(2)ThH](2), shows that the thorium(4+) to thorium(3+) hydride interconversion reaction is endothermic by 26 kcal/mol.

  6. The (impossible?) formation of acetaldehyde on the grain surfaces: insights from quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Enrique-Romero, J.; Rimola, A.; Ceccarelli, C.; Balucani, N.

    2016-06-01

    Complex Organic Molecules (COMs) have been detected in the interstellar medium (ISM). However, it is not clear whether their synthesis occurs on the icy surfaces of interstellar grains or via a series of gas-phase reactions. As a test case of the COMs synthesis in the ISM, we present new quantum chemical calculations on the formation of acetaldehyde (CH3CHO) from the coupling of the HCO and CH3 radicals, both in gas phase and on water ice surfaces. The binding energies of HCO and CH3 on the amorphous water ice were also computed (2333 and 734 K, respectively). Results indicate that, in gas phase, the products could be either CH3CHO, CH4 + CO, or CH3OCH, depending on the relative orientation of the two radicals. However, on the amorphous water ice, only the CH4 + CO product is possible due to the geometrical constraints imposed by the water ice surface. Therefore, acetaldehyde cannot be synthesized by the CH3 + HCO coupling on the icy grains. We discuss the implications of these results and other cases, such as ethylene glycol and dimethyl ether, in which similar situations can occur, suggesting that formation of these molecules on the grain surfaces might be unlikely.

  7. Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach.

    PubMed

    Zapata-Torres, Gerald; Fierro, Angélica; Barriga-González, German; Salgado, J Cristian; Celis-Barros, Cristian

    2015-07-27

    Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophilic and hydride transfer, were addressed in order to comprehend the nature of their rate-determining step. The Quantum Chemical Cluster Approach was used to obtain transition states of MAO B complexed with phenylethylamine (PEA), benzylamine (BA), and p-nitrobenzylamine (NBA). The choice of these amines relies on their importance to address MAO B catalytic mechanisms so as to help us to answer questions such as why BA is a better substrate than NBA or how para-substitution affects substrate's reactivity. Transition states were later validated by comparison with the experimental free energy barriers. From a theoretical point of view, and according to the our reported transition states, their calculated barriers and structural and orbital differences obtained by us among these compounds, we propose that good substrates such as BA and PEA might follow the hydride transfer pathway while poor substrates such as NBA prefer the polar nucleophilic mechanism, which might suggest that MAO B can act by both mechanisms. The low free energy barriers for BA and PEA reflect the preference that MAO B has for hydride transfer over the polar nucleophilic mechanism when catalyzing the oxidative deamination of neurotransmitters.

  8. Synthesis, structural characterization and quantum chemical studies of silicon-containing benzoic acid derivatives

    NASA Astrophysics Data System (ADS)

    Zaltariov, Mirela-Fernanda; Cojocaru, Corneliu; Shova, Sergiu; Sacarescu, Liviu; Cazacu, Maria

    2016-09-01

    The present paper is concerned with the synthesis and molecular structure investigation of two new benzoic acid derivatives having trimethylsilyl tails, 4-((trimethylsilyl)methoxy) and 4-(3-(trimethylsilyl)propoxy)benzoic acids. The structures of the novel compounds have been confirmed by X-ray crystallography, Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (1H and 13C NMR). The theoretical studies of molecules were conducted by using the quantum chemical methods, such as Density Functional Theory (DFT B3LYP/6-31 + G**), Hartree-Fock (HF/6-31 + G**) and semiempirical computations (PM3, PM6 and PM7). The optimized molecular geometries have been found to be in good agreement with experimental structures resulted from the X-ray diffraction. The maximum electronic absorption bands observed at 272-287 nm (UV-vis spectra) have been assigned to π → π* transitions, which were in reasonable agreement with the time dependent density functional theory (TD-DFT) calculations. The computed vibrational frequencies by DFT method were assigned and compared with the experimental FTIR spectra. The mapped electrostatic potentials revealed the reactive sites, which corroborated the observation of the dimer supramolecular structures formed in the crystals by hydrogen-bonding. The energies of frontier molecular orbitals (HOMO and LUMO), energy gap, dipole moment and molecular descriptors for the new compounds were calculated and discussed.

  9. Quantum Chemical Insight into the Interactions and Thermodynamics Present in Choline Chloride Based Deep Eutectic Solvents.

    PubMed

    Wagle, Durgesh V; Deakyne, Carol A; Baker, Gary A

    2016-07-14

    We report quantum chemical calculations performed on three popular deep eutectic solvents (DESs) in order to elucidate the molecular interactions, charge transfer interactions, and thermodynamics associated with these systems. The DESs studied comprise 1:2 choline chloride/urea (reline), 1:2 choline chloride/ethylene glycol (ethaline), and 1:1 choline chloride/malonic acid (maloline). The excellent correlation between calculated and experimental vibrational spectra allowed for identification of dominant interactions in the DES systems. The DESs were found to be stabilized by both conventional hydrogen bonds and C-H···O/C-H···π interactions between the components. The hydrogen-bonding network established in the DES is clearly distinct from that which exists within the neat hydrogen-bond donor dimer. Charge decomposition analysis indicates significant charge transfer from choline and chloride to the hydrogen-bond donor with a higher contribution from the cation, and a density of states analysis confirms the direction of the charge transfer. Consequently, the sum of the bond orders of the choline-Cl(-) interactions in the DESs correlates directly with the melting temperatures of the DESs, a correlation that offers insight into the effect of the tuning of the choline-Cl(-) interactions by the hydrogen-bond donors on the physical properties of the DESs. Finally, the differences in the vibrational entropy changes upon DES formation are consistent with the trend in the overall entropy changes upon DES formation. PMID:27268431

  10. Quantum chemical and experimental study of 1,2,4-trihydroxy-para-menthane

    NASA Astrophysics Data System (ADS)

    Rottmannová, Lenka; Lukeš, Vladimír; Ilčin, Michal; Fodran, Peter; Herich, Peter; Kožíšek, Jozef; Liptaj, Tibor; Klein, Erik

    2013-10-01

    The conformational analysis of the para-menthane (PM) and 1,2,4-trihydroxy-para-menthane (TPM) is performed using the quantum chemical density functional theory (DFT) and ab initio Møller-Plesset perturbation theory up to the second order (MP2). In TPM, three hydroxyl groups generate eight stereoisomers comparing to the four para-menthane stereoisomers. From the thermodynamics point of view, the most preferred conformations show the chair-shaped configuration of the cyclohexane ring. The obtained energy barriers for the isopropyl group rotation in the chair-shaped stereoisomers are between 35 and 45 kJ mol-1. The crystal structure as well as the solvated TPM stereoisomer isolated from the Tea tree oil, Melaleuca alternifolia (Maiden & Betche) Cheel, were investigated experimentally. Isolated stereoisomer corresponds to the most energetically preferred conformation and the calculated structural data agree very well with the results from the X-ray and nuclear magnetic resonance measurements. Finally, the influence of the conformation and the presence of the intramolecular hydrogen bonds on the homolytic Osbnd H bond dissociation enthalpies and proton affinities were also discussed with respect to the simple alcohols (methanol, iso-propanol, iso-pentanol, tert-butanol, cyclohexanol) and phenol.

  11. Intramolecular hydrogen bonding in 5-nitrosalicylaldehyde: IR spectrum and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Moosavi-Tekyeh, Zainab; Taherian, Fatemeh; Tayyari, Sayyed Faramarz

    2016-05-01

    The structural parameters, and vibrational frequencies of 5-nitrosalicylaldehyde (5NSA) were studied by the FT-IR and Raman spectra and the quantum chemical calculations carried out at the B3LYP/6-311++G(d,p) level of theory in order to investigate the intramolecular hydrogen bonding (IHB) present in its structure. The strength and nature of IHB in the optimized structure of 5NSA were studied in detail by means of the atoms in molecules (AIM) and the natural bond orbital (NBO) approaches. The results obtained were then compared with the corresponding data for its parent molecule, salicylaldehyde (SA). Comparisons made between the geometrical structures for 5NSA and SA, their OH/OD stretching and out-of-plane bending modes, their enthalpies for the hydrogen bond, and their AIM parameters demonstrated a stronger H-bonding in 5NSA compared with that in SA. The calculated binding enthalpy (ΔHbind) for 5NSA was -10.92 kcal mol-1. The observed νOH and γOH appeared at about 3120 cm-1 and 786 cm-1 respectively. The stretching frequency shift of H-bond formation was 426 cm-1 which is consistent with ΔHbind and the strength of H-bond in 5NSA. The delocalization energies and electron delocalization indices derived by the NBO and AIM approaches indicate that the resonance effects were responsible for the stronger IHB in 5NSA than in SA.

  12. The mechanisms of action of cAMP. A quantum chemical study.

    PubMed

    van Ool, P J; Buck, H M

    1982-01-01

    Quantum chemical calculations were performed on the formation of intermediates with trigonal bipyramidal (TBP) configurations in the hydrolysis of adenosine 3',5'-monophosphate (cAMP) with phosphodiesterases and the activation of protein kinases by cAMP. The results show that in the reaction sequence concerning the hydrolysis of cAMP with phosphodiesterase the TBP intermediate must possess an equatorial-apical cyclic phosphate ring with the 3'-oxygen atom in the apical position. This could be an additional reason for the sensitivity of the 3' position in cAMP towards modifications in comparison with the 5' position. According to the calculations, a mechanistic model is presented for the enzymatic hydrolysis of cAMP with the involvement of a covalently bonded enzyme-nucleotide intermediate. Also a model is offered for the activation of protein kinase by cAMP. The activation of protein kinase is assumed to proceed via diequatorial-ring-positioned TBP intermediates resulting in the formation of a covalent bond between cAMP and the protein kinase with retention of the cyclic phosphate ring. It seems likely that the enzyme-nucleotide intermediate enforces a conformational change in the enzyme, which causes the dissociation of the regulatory and catalytic subunit of the protein kinase, necessary for a physiological response.

  13. Redox potential of the Rieske iron-sulfur protein quantum-chemical and electrostatic study.

    PubMed

    Kuznetsov, Andrey M; Zueva, Ekaterina M; Masliy, Alexei N; Krishtalik, Lev I

    2010-03-01

    Quantum-chemical study of structures, energies, and effective partial charge distribution for several models of the Rieske protein redox center is performed in terms of the B3LYP density functional method in combination with the broken symmetry approach using three different atomic basis sets. The structure of the redox complex optimized in vacuum differs markedly from that inside the protein. This means that the protein matrix imposes some stress on the active site resulting in distortion of its structure. The redox potentials calculated for the real active site structure are in a substantially better agreement with the experiment than those calculated for the idealized structure. This shows an important role of the active site distortion in tuning its redox potential. The reference absolute electrode potential of the standard hydrogen electrode is used that accounts for the correction caused by the water surface potential. Electrostatic calculations are performed in the framework of the polarizable solute model. Two dielectric permittivities of the protein are employed: the optical permittivity for calculation of the intraprotein electric field, and the static permittivity for calculation of the dielectric response energy. Only this approach results in a reasonable agreement of the calculated and experimental redox potentials.

  14. Effect of the Titanium Nanoparticle on the Quantum Chemical Characterization of the Liquid Sodium Nanofluid.

    PubMed

    Suzuki, Ai; Bonnaud, Patrick; Williams, Mark C; Selvam, Parasuraman; Aoki, Nobutoshi; Miyano, Masayuki; Miyamoto, Akira; Saito, Jun-ichi; Ara, Kuniaki

    2016-04-14

    Suspension state of a titanium nanoparticle in the liquid sodium was quantum chemically characterized by comparing physical characteristics, viz., electronic state, viscosity, and surface tension, with those of liquid sodium. The exterior titanium atoms on the topmost facet of the nanoparticle were found to constitute a stable Na-Ti layer, and the Brownian motion of a titanium nanoparticle could be seen in tandem with the surrounding sodium atoms. An electrochemical gradient due to the differences in electronegativity of both titanium and sodium causes electron flow from liquid sodium atoms to a titanium nanoparticle, Ti + Na → Ti(δ-) + Na(δ+), making the exothermic reaction possible. In other words, the titanium nanoparticle takes a role as electron-reservoir by withdrawing free electrons from sodium atoms and makes liquid sodium electropositive. The remaining electrons in the liquid sodium still make Na-Na bonds and become more stabilized. With increasing size of the titanium nanoparticle, the deeper electrostatic potential, the steeper electric field, and the larger Debye atmosphere are created in the electric double layer shell. Owing to electropositive sodium-to-sodium electrostatic repulsion between the external shells, naked titanium nanoparticles cannot approach each other, thus preventing the agglomeration. PMID:27008416

  15. A study of the molecular, vibrational, electronic and quantum chemical investigation of 2-methyl-1-vinylimidazole

    NASA Astrophysics Data System (ADS)

    John Xavier, R.; Dinesh, P.

    2015-02-01

    The spectroscopic properties of 2-methyl-1-vinylimidazole (abbreviated as 2M1VIM) were examined by FT-IR, FT-Raman and NMR techniques. FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm-1 and 3500-50 cm-1, respectively. The 1H and 13C NMR spectra were recorded in CDCl3. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional theory (DFT) employing B3LYP and LSDA methods with 6-311++G(d,p) basis set. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibration were assigned on the basis of potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanical (SQM) method. The optimized structure of the compound was interpreted and compared with the reported experimental values. The observed vibrational ware numbers, absorption wavelengths and chemical shifts were compared with calculated values. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. As a result, the optimized geometry, and calculated spectroscopic data show a good agreement with the experimental results.

  16. A study of the molecular, vibrational, electronic and quantum chemical investigation of 2-methyl-1-vinylimidazole.

    PubMed

    John Xavier, R; Dinesh, P

    2015-02-01

    The spectroscopic properties of 2-methyl-1-vinylimidazole (abbreviated as 2M1VIM) were examined by FT-IR, FT-Raman and NMR techniques. FT-IR and FT-Raman spectra were recorded in the region 4000-400cm(-1) and 3500-50cm(-1), respectively. The (1)H and (13)C NMR spectra were recorded in CDCl3. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional theory (DFT) employing B3LYP and LSDA methods with 6-311++G(d,p) basis set. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibration were assigned on the basis of potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanical (SQM) method. The optimized structure of the compound was interpreted and compared with the reported experimental values. The observed vibrational ware numbers, absorption wavelengths and chemical shifts were compared with calculated values. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. As a result, the optimized geometry, and calculated spectroscopic data show a good agreement with the experimental results. PMID:25459718

  17. Structural and quantum chemical studies of 8-aryl-sulfanyl adenine class Hsp90 inhibitors.

    PubMed

    Immormino, Robert M; Kang, Yanlong; Chiosis, Gabriela; Gewirth, Daniel T

    2006-08-10

    Hsp90 chaperones play a critical role in modulating the activity of many cell signaling proteins and are an attractive target for anti-cancer therapeutics. We report here the structures of the water soluble 8-aryl-sulfanyl adenine class Hsp90 inhibitors, 1 (PU-H71) and 2 (PU-H64), in complex with the N-terminal domain of human Hsp90alpha. The conformation of 1 when bound to Hsp90 differs from previously reported 8-aryl adenine Hsp90 inhibitors including 3 (PU24FCl). While the binding mode for 3 places the 2'-halide of the 8-aryl group on top of the adenine ring, for 1 and 2, we show that the 2'-halide is rotated approximately 180 degrees away. This difference explains the opposing trends in Hsp90 inhibitory activity for the 2'-halo derivatives of the 3',4',5'-trimethoxy series where Cl > Br > I compared to the 4',5'-methylenedioxy series where I > Br > Cl. We also present quantum chemical calculations of 2 and its analogues that illuminate their basis for Hsp90 inhibition. The calculated conformation of 2 agreed well with the crystallographically observed conformations of 1 and 2. The predictive nature of the calculations has allowed the exploration of additional derivatives based on the 8-aryl adenine scaffold.

  18. The dynamic behavior of a liquid ethanol-water mixture: a perspective from quantum chemical topology.

    PubMed

    Mejía, Sol M; Mills, Matthew J L; Shaik, Majeed S; Mondragon, Fanor; Popelier, Paul L A

    2011-05-01

    Quantum Chemical Topology (QCT) is used to reveal the dynamics of atom-atom interactions in a liquid. A molecular dynamics simulation was carried out on an ethanol-water liquid mixture at its azeotropic concentration (X(ethanol)=0.899), using high-rank multipolar electrostatics. A thousand (ethanol)(9)-water heterodecamers, respecting the water-ethanol ratio of the azeotropic mixture, were extracted from the simulation. Ab initio electron densities were computed at the B3LYP/6-31+G(d) level for these molecular clusters. A video shows the dynamical behavior of a pattern of bond critical points and atomic interaction lines, fluctuating over 1 ns. A bond critical point distribution revealed the fluctuating behavior of water and ethanol molecules in terms of O-H···O, C-H···O and H···H interactions. Interestingly, the water molecule formed one to six C-H···O and one to four O-H···O interactions as a proton acceptor. We found that the more localized a dynamical bond critical point distribution, the higher the average electron density at its bond critical points. The formation of multiple C-H···O interactions affected the shape of the oxygen basin of the water molecule, which is shown in three dimensions. The hydrogen atoms of water strongly preferred to form H···H interactions with ethanol's alkyl hydrogen atoms over its hydroxyl hydrogen.

  19. New insights in quantum chemical topology studies using numerical grid-based analyses.

    PubMed

    Kozlowski, David; Pilmé, Julien

    2011-11-30

    New insights in Quantum Chemical Topology of one-electron density functions have been proposed here by using a recent grid-based algorithm (Tang et al., J Phys Condens Matter 2009, 21, 084204), initially designed for the decomposition of the electron density. Beyond the charge analysis, we show that this algorithm is suitable for different scalar functions showing a more complex topology, that is, the Laplacian of the electron density, the electron localization function (ELF), and the molecular electrostatic potential (MEP). This algorithm makes use of a robust methodology enabling to numerically assign the data points of three-dimensional grids to basin volumes, and it has the advantage of requiring only the values of the scalar function without details on the wave function used to build the grid. Our implementation is briefly outlined (program named TopChem), its capabilities are examined, and technical aspects in terms of CPU requirement and accuracy of the results are discussed. Illustrative examples for individual molecules and crystalline solids obtained with gaussian and plane-wave-based density functional theory calculations are presented. Special attention was given to the MEP because its topological analysis is complex and scarce.

  20. Chemical shifts in biomolecules

    PubMed Central

    Case, David A.

    2013-01-01

    Summary NMR chemical shifts are sensitive probes of stucture and dynamics in proteins. Empirical models, based on a large database of measured shifts, take an input structure and provide increasingly accurate estimates of the corresponding shifts. Quantum chemical calculations can provide the same information, with greater generality but (currently) with less accuracy. These methods are now providing new ways to approach NMR structure determination, and new insights into the conformational dynamics of proteins. PMID:23422068

  1. Low temperature rate constants for the N + CN → N2 + C reaction: two-dimensional quantum capture calculations on an accurate potential energy surface.

    PubMed

    Ma, Jianyi; Guo, Hua; Dawes, Richard

    2012-09-21

    The title reaction is thought to be responsible for the production of molecular nitrogen in interstellar clouds. In this work, we report quantum capture calculations on a new two-dimensional potential energy surface determined by interpolating high-level ab initio data. The low-temperature rate constant calculated using a capture model is quite large and has a positive temperature dependence, in agreement with a recent experiment. The origin of the aforementioned behaviors of the rate constant is analyzed.

  2. Kinetic-quantum chemical model for catalytic cycles: the Haber-Bosch process and the effect of reagent concentration.

    PubMed

    Kozuch, Sebastian; Shaik, Sason

    2008-07-01

    A combined kinetic-quantum chemical model is developed with the goal of estimating in a straightforward way the turnover frequency (TOF) of catalytic cycles, based on the state energies obtained by quantum chemical calculations. We describe how the apparent activation energy of the whole cycle, so-called energetic span (delta E), is influenced by the energy levels of two species: the TOF determining transition state (TDTS) and the TOF determining intermediate (TDI). Because these key species need not be adjoining states, we conclude that for catalysis there are no rate-determining steps, only rate determining states. In addition, we add here the influence of reactants concentrations. And, finally, the model is applied to the Haber-Bosch process of ammonia synthesis, for which we show how to calculate which catalyst will be the most effective under specific reagents conditions.

  3. Structural and vibrational spectral investigations of melaminium maleate monohydrate by FTIR, FT-Raman and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

    2013-04-01

    The structural investigations of the molecular complex of melamine with maleic acid, namely melaminium maleate monohydrate have been carried out by quantum chemical methods in addition to FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical studies were performed with DFT (B3LYP) method using 6-31G**, cc-pVDZ and 6-311++G** basis sets to determine the energy, structural and thermodynamic parameters of melaminium maleate monohydrate. The hydrogen atom from maleic acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H⋯O and Nsbnd H⋯O hydrogen bonds shows notable vibrational effects.

  4. The pyrolysis of 2-methylfuran: a quantum chemical, statistical rate theory and kinetic modelling study.

    PubMed

    Somers, Kieran P; Simmie, John M; Metcalfe, Wayne K; Curran, Henry J

    2014-03-21

    Due to the rapidly growing interest in the use of biomass derived furanic compounds as potential platform chemicals and fossil fuel replacements, there is a simultaneous need to understand the pyrolysis and combustion properties of such molecules. To this end, the potential energy surfaces for the pyrolysis relevant reactions of the biofuel candidate 2-methylfuran have been characterized using quantum chemical methods (CBS-QB3, CBS-APNO and G3). Canonical transition state theory is employed to determine the high-pressure limiting kinetics, k(T), of elementary reactions. Rice-Ramsperger-Kassel-Marcus theory with an energy grained master equation is used to compute pressure-dependent rate constants, k(T,p), and product branching fractions for the multiple-well, multiple-channel reaction pathways which typify the pyrolysis reactions of the title species. The unimolecular decomposition of 2-methylfuran is shown to proceed via hydrogen atom transfer reactions through singlet carbene intermediates which readily undergo ring opening to form collisionally stabilised acyclic C5H6O isomers before further decomposition to C1-C4 species. Rate constants for abstraction by the hydrogen atom and methyl radical are reported, with abstraction from the alkyl side chain calculated to dominate. The fate of the primary abstraction product, 2-furanylmethyl radical, is shown to be thermal decomposition to the n-butadienyl radical and carbon monoxide through a series of ring opening and hydrogen atom transfer reactions. The dominant bimolecular products of hydrogen atom addition reactions are found to be furan and methyl radical, 1-butene-1-yl radical and carbon monoxide and vinyl ketene and methyl radical. A kinetic mechanism is assembled with computer simulations in good agreement with shock tube speciation profiles taken from the literature. The kinetic mechanism developed herein can be used in future chemical kinetic modelling studies on the pyrolysis and oxidation of 2-methylfuran

  5. Quantum chemical characterization of zwitterionic structures: Supramolecular complexes for modifying the wettability of oil-water-limestone system.

    PubMed

    Lopez-Chavez, Ernesto; Garcia-Quiroz, Alberto; Gonzalez-Garcia, Gerardo; Orozco-Duran, Gabriela E; Zamudio-Rivera, Luis S; Martinez-Magadan, José M; Buenrostro-Gonzalez, Eduardo; Hernandez-Altamirano, Raul

    2014-06-01

    In this work, we present a quantum chemical study pertaining to some supramolecular complexes acting as wettability modifiers of oil-water-limestone system. The complexes studied are derived from zwitterionic liquids of the types N'-alkyl-bis, N-alquenil, N-cycloalkyl, N-amyl-bis-beta amino acid or salts acting as sparkling agents. We studied two molecules of zwitterionic liquids (ZL10 and ZL13), HOMO and LUMO levels, and the energy gap between them, were calculated, as well as the electron affinity (EA) and ionization potential (IP), chemical potential, chemical hardness, chemical electrophilicity index and selectivity descriptors such Fukui indices. In this work, electrochemical comparison was realized with cocamidopropyl betaine (CPB), which is a structure zwitterionic liquid type, nowadays widely applied in enhanced recovery processes.

  6. Accurate theoretical chemistry with coupled pair models.

    PubMed

    Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan

    2009-05-19

    Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now

  7. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

    Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

    2009-07-14

    A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol.

  8. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

    Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

    2009-07-14

    A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol. PMID:19603962

  9. Full-dimensional quantum calculations of vibrational levels of NH4+ and isotopomers on an accurate ab initio potential energy surface

    DOE PAGES

    Hua -Gen Yu; Han, Huixian; Guo, Hua

    2016-03-29

    Vibrational energy levels of the ammonium cation (NH4+) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4+ and ND4+ exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm–1.

  10. Full-Dimensional Quantum Calculations of Vibrational Levels of NH4(+) and Isotopomers on An Accurate Ab Initio Potential Energy Surface.

    PubMed

    Yu, Hua-Gen; Han, Huixian; Guo, Hua

    2016-04-14

    Vibrational energy levels of the ammonium cation (NH4(+)) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4(+) and ND4(+) exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. The low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm(-1).

  11. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    PubMed

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

    2016-05-17

    Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

  12. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    PubMed

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

    2016-05-17

    Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

  13. Chemically differentiating ascorbate-mediated dissolution of quantum dots in cell culture media

    NASA Astrophysics Data System (ADS)

    Su, Cheng-Kuan; Sun, Yuh-Chang

    2013-02-01

    To investigate the dynamic dissolution of quantum dots (QDs) in cell culture media, in this study we constructed an online automatic analytical system comprising a sequential in-tube solid phase extraction (SPE) device and an inductively coupled plasma (ICP) mass spectrometer. By means of selectively extracting QDs and cadmium ions (Cd2+) onto the interior surface of the polytetrafluoroethylene (PTFE) tube, this novel SPE device could be used to determine the degree of QD dissolution through a simple adjustment of sample acidity. To the best of our knowledge, this study is the first to exploit PTFE tubing as a selective SPE adsorbent for the online chemical differentiation of QDs and Cd2+ ions with the goal of monitoring the phenomenon of QD dissolution in complicated biological matrices. We confirmed the analytical reliability of this system through comparison of the measured Cd-to-QD ratios to the expected values. When analyzing QDs and Cd2+ ions at picomolar levels, a temporal resolution of 8 min was required to load sufficient amounts of the analytes to meet the sensitivity requirements of the ICP mass spectrometer. To demonstrate the practicability of this developed method, we measured the dynamic variations in the Cd-to-QD705 ratio in the presence of ascorbate as a physiological stimulant to generate reactive oxygen species in cell culture media and trigger the dissolution of QDs; our results suggest that the ascorbate-induced QD dissolution was dependent on the time, treatment concentration, and nature of the biomolecule.To investigate the dynamic dissolution of quantum dots (QDs) in cell culture media, in this study we constructed an online automatic analytical system comprising a sequential in-tube solid phase extraction (SPE) device and an inductively coupled plasma (ICP) mass spectrometer. By means of selectively extracting QDs and cadmium ions (Cd2+) onto the interior surface of the polytetrafluoroethylene (PTFE) tube, this novel SPE device could be

  14. Electronic transitions in liquid amides studied by using attenuated total reflection far-ultraviolet spectroscopy and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Morisawa, Yusuke; Yasunaga, Manaka; Fukuda, Ryoichi; Ehara, Masahiro; Ozaki, Yukihiro

    2013-10-01

    Attenuated total reflection far-ultraviolet (ATR-FUV) spectra in the 140-260 nm region were measured for several types of liquid amides (formamide, FA; N-methylformamide, NMF; N-methylacetamide, NMA; N,N-dimethylformamide, NdMF; and N,N-dimethylacetamide, NdMA) to investigate their electronic transitions in the FUV region. The spectra were compared with the corresponding gas-phase spectra to examine the shift in the major absorption band in the 180-200 nm region going from the gas phase to the liquid phase, and it was found that the peak shift was dependent on the particular amide. FA and NMF, which exhibit intermolecular C=O…H-N hydrogen bonding, show a large shift of ˜0.60 eV to lower energy; however, NMA, which also exhibits hydrogen bonding, shows only a small shift. In NdMF and NdMA, C=O groups seem to be coupled, which results in a small peak shift. Two types of quantum chemical calculations, time-dependent density functional theory (TD-DFT) and symmetry-adapted-cluster configuration interaction (SAC-CI) method, were performed to elucidate the origin of the shifts and the band assignments. The shift estimated by the monomer and dimer models with TD-DFT reproduced well the observed shift from the gas phase to the liquid phase. This suggests that the intermolecular hydrogen-bonding interaction significantly affects the magnitude of the shift. The many-body effects were also considered using the larger cluster models (trimer to pentamer). The energy shift calculated using SAC-CI with the monomer and the state-specific polarizable continuum model was also accurate, indicating that the nonlinear polarization effect appears to be important. As for the band assignments, it was found that though the major band can be mainly attributed to the π-π* transition, several types of Rydberg transitions also exist in its vicinity and mixing of orbitals with the same symmetry occurs. The number and type of Rydberg transitions in the spectra depend upon the type of amide

  15. Photophysics of α-furil at room temperature and 77 K: Spectroscopic and quantum chemical studies.

    PubMed

    Kundu, Pronab; Chattopadhyay, Nitin

    2016-06-21

    Steady state and time resolved spectroscopic measurements have been exploited to assign the emissions from different conformations of α-furil (2, 2'-furil) in solution phase at room temperature as well as cryogen (liquid nitrogen, LN2) frozen matrices of ethanol and methylcyclohexane. Room temperature studies reveal a single fluorescence from the trans-planar conformer of the fluorophore or two fluorescence bands coming from the trans-planar and the relaxed skew forms depending on excitation at the nπ(∗) or the ππ(∗) absorption band, respectively. Together with the fluorescence bands, the LN2 studies in both the solvents unambiguously ascertain two phosphorescence emissions with lifetimes 5 ± 0.3 ms (trans-planar triplet) and 81 ± 3 ms (relaxed skew triplet). Quantum chemical calculations have been performed using density functional theory at CAM-B3LYP/6-311++G(∗∗) level to prop up the spectroscopic surveillance. The simulated potential energy curves (PECs) illustrate that α-furil is capable of giving two emissions from each of the S1 and the T1 states-one corresponding to the trans-planar and the other to the relaxed skew conformation. Contrary to the other 1,2-dicarbonyl molecular systems like benzil and α-naphthil, α-furil does not exhibit any fluorescence from its second excited singlet (S2) state. This is ascribed to the proximity of the minimum of the PEC of the S2 state and the hill-top of the PEC of the S1 state. PMID:27334172

  16. Photophysics of α-furil at room temperature and 77 K: Spectroscopic and quantum chemical studies

    NASA Astrophysics Data System (ADS)

    Kundu, Pronab; Chattopadhyay, Nitin

    2016-06-01

    Steady state and time resolved spectroscopic measurements have been exploited to assign the emissions from different conformations of α-furil (2, 2'-furil) in solution phase at room temperature as well as cryogen (liquid nitrogen, LN2) frozen matrices of ethanol and methylcyclohexane. Room temperature studies reveal a single fluorescence from the trans-planar conformer of the fluorophore or two fluorescence bands coming from the trans-planar and the relaxed skew forms depending on excitation at the nπ∗ or the ππ∗ absorption band, respectively. Together with the fluorescence bands, the LN2 studies in both the solvents unambiguously ascertain two phosphorescence emissions with lifetimes 5 ± 0.3 ms (trans-planar triplet) and 81 ± 3 ms (relaxed skew triplet). Quantum chemical calculations have been performed using density functional theory at CAM-B3LYP/6-311++G∗∗ level to prop up the spectroscopic surveillance. The simulated potential energy curves (PECs) illustrate that α-furil is capable of giving two emissions from each of the S1 and the T1 states - one corresponding to the trans-planar and the other to the relaxed skew conformation. Contrary to the other 1,2-dicarbonyl molecular systems like benzil and α-naphthil, α-furil does not exhibit any fluorescence from its second excited singlet (S2) state. This is ascribed to the proximity of the minimum of the PEC of the S2 state and the hill-top of the PEC of the S1 state.

  17. Quantum Chemical Study on ·Cl-Initiated Atmospheric Degradation of Monoethanolamine.

    PubMed

    Xie, Hong-Bin; Ma, Fangfang; Wang, Yuanfang; He, Ning; Yu, Qi; Chen, Jingwen

    2015-11-17

    Recent findings on the formation of ·Cl in continental urban areas necessitate the consideration of ·Cl initiated degradation when assessing the fate of volatile organic pollutants. Monoethanolamine (MEA) is considered as a potential atmospheric pollutant since it is a benchmark and widely utilized solvent in a leading CO2 capture technology. Especially, ·Cl may have specific interactions with the N atom of MEA, which could make the MEA + ·Cl reaction have different pathways and products from those of the MEA + ·OH reaction. Hence, ·Cl initiated reactions with MEA were investigated by a quantum chemical method [CCSD(T)/aug-cc-pVTZ//MP2/6-31+G(3df,2p)] and kinetics modeling. Results show that the overall rate constant for ·Cl initiated H-abstraction of MEA is 5 times faster than that initiated by ·OH, and the tropospheric lifetimes of MEA will be overestimated by 6-46% when assuming that [·Cl]/[·OH] = 1-10% if the role of ·Cl is ignored. The MEA + ·Cl reaction exclusively produces MEA-N that finally transforms into several products including mutagenic nitramine and carcinogenic nitrosamine via further reactions with O2/NOx, and the contribution of ·Cl to their formation is about 25-250% of that of ·OH. Thus, it is necessary to consider ·Cl initiated tropospheric degradation of MEA for its risk assessment. PMID:26495768

  18. Study of polymorphism in imatinib mesylate: A quantum chemical approach using electronic and vibrational spectra

    NASA Astrophysics Data System (ADS)

    Srivastava, Anubha; Joshi, B. D.; Tandon, Poonam; Ayala, A. P.; Bansal, A. K.; Grillo, Damián

    2013-02-01

    Imatinib mesylate, 4-(4-methyl-piperazin-1-ylmethyl)-N-u[4-methyl-3-(4-pyridin-3-yl)pyrimidine-2-ylamino)phenyl]benzamide methanesulfonate is a therapeutic drug that is approved for the treatment of chronic myelogeneous leukemia (CML) and gastrointestinal stromal tumors (GIST). It is known that imatinib mesylate exists in two polymorphic forms α and β. However, β-form is more stable than the α-form. In this work, we present a detailed vibrational spectroscopic investigation of β-form by using FT-IR and FT-Raman spectra. These data are supported by quantum mechanical calculations using DFT employing 6-311G(d,p) basis set, which allow us to characterize completely the vibrational spectra of this compound. The FT-IR spectrum of α-form has also been discussed. The importance of hydrogen-bond formation in the molecular packing arrangements of both forms has been examined with the vibrational shifts observed due to polymorphic changes. The red shift of the NH stretching bands in the infrared spectrum from the computed wavenumber indicates the weakening of the NH bond. The UV-vis spectroscopic studies along with the HOMO-LUMO analysis of both polymorphs (α and β) were performed and their chemical activity has been discussed. The TD-DFT method was used to calculate the electronic absorption spectra in the gas phase as well as in the solvent environment using IEF-PCM model and 6-31G basis set. Finally, the results obtained complements to the experimental findings.

  19. Thermal Decomposition of NCN: Shock-Tube Study, Quantum Chemical Calculations, and Master-Equation Modeling.

    PubMed

    Busch, Anna; González-García, Núria; Lendvay, György; Olzmann, Matthias

    2015-07-16

    The thermal decomposition of cyanonitrene, NCN, was studied behind reflected shock waves in the temperature range 1790-2960 K at pressures near 1 and 4 bar. Highly diluted mixtures of NCN3 in argon were shock-heated to produce NCN, and concentration-time profiles of C atoms as reaction product were monitored with atomic resonance absorption spectroscopy at 156.1 nm. Calibration was performed with methane pyrolysis experiments. Rate coefficients for the reaction (3)NCN + M → (3)C + N2 + M (R1) were determined from the initial slopes of the C atom concentration-time profiles. Reaction R1 was found to be in the low-pressure regime at the conditions of the experiments. The temperature dependence of the bimolecular rate coefficient can be expressed with the following Arrhenius equation: k1(bim) = (4.2 ± 2.1) × 10(14) exp[-242.3 kJ mol(-1)/(RT)] cm(3) mol(-1) s(-1). The rate coefficients were analyzed by using a master equation with specific rate coefficients from RRKM theory. The necessary molecular data and energies were calculated with quantum chemical methods up to the CCSD(T)/CBS//CCSD/cc-pVTZ level of theory. From the topography of the potential energy surface, it follows that reaction R1 proceeds via isomerization of NCN to CNN and subsequent C-N bond fission along a collinear reaction coordinate without a tight transition state. The calculations reproduce the magnitude and temperature dependence of the rate coefficient and confirm that reaction R1 is in the low-pressure regime under our experimental conditions.

  20. Theoretical prediction of hydrogen-bond basicity pKBHX using quantum chemical topology descriptors.

    PubMed

    Green, Anthony J; Popelier, Paul L A

    2014-02-24

    Hydrogen bonding plays an important role in the interaction of biological molecules and their local environment. Hydrogen-bond strengths have been described in terms of basicities by several different scales. The pKBHX scale has been developed with the interests of medicinal chemists in mind. The scale uses equilibrium constants of acid···base complexes to describe basicity and is therefore linked to Gibbs free energy. Site specific data for polyfunctional bases are also available. The pKBHX scale applies to all hydrogen-bond donors (HBDs) where the HBD functional group is either OH, NH, or NH+. It has been found that pKBHX can be described in terms of a descriptor defined by quantum chemical topology, ΔE(H), which is the change in atomic energy of the hydrogen atom upon complexation. Essentially the computed energy of the HBD hydrogen atom correlates with a set of 41 HBAs for five common HBDs, water (r2=0.96), methanol (r2=0.95), 4-fluorophenol (r2=0.91), serine (r2=0.93), and methylamine (r2=0.97). The connection between experiment and computation was strengthened with the finding that there is no relationship between ΔE(H) and pKBHX when hydrogen fluoride was used as the HBD. Using the methanol model, pKBHX predictions were made for an external set of bases yielding r2=0.90. Furthermore, the basicities of polyfunctional bases correlate with ΔE(H), giving r2=0.93. This model is promising for the future of computation in fragment-based drug design. Not only has a model been established that links computation to experiment, but the model may also be extrapolated to predict external experimental pKBHX values.

  1. Chemical Control of Lead Sulfide Quantum Dot Shape, Self-Assembly, and Charge Transport

    NASA Astrophysics Data System (ADS)

    McPhail, Martin R.

    Lead(II) sulfide quantum dots (PbS QDs) are a promising excitonic material for numerous application that require that control of fluxes of charge and energy at nanoscale interfaces, such as solar energy conversion, photo- and electrocatalysis, light emitting diodes, chemical sensing, single-electron logic elements, field effect transistors, and photovoltaics. PbS QDs are particularly suitable for photonics applications because they exhibit size-tunable band-edge absorption and fluorescence across the entire near-infrared spectrum, undergo efficient multi-exciton generation, exhibit a long radiative lifetime, and possess an eight-fold degenerate ground-state. The effective integration of PbS QDs into these applications requires a thorough understanding of how to control their synthesis, self-assembly, and charge transport phenomena. In this document, I describe a series of experiments to elucidate three levels of chemical control on the emergent properties of PbS QDs: (1) the role of surface chemistry in controlling PbS QD shape during solvothermal synthesis, (2) the role of QD shape and ligand functionalization in self-assembly at a liquid-air interface, and (3) the role of QD packing structure on steady-state conductivity and transient current dynamics. At the synthetic level (1), I show that the final shape and surface chemistry of PbS QDs is highly sensitive to the formation of organosulfur byproducts by commonly used sulfur reagents. The insight into PbS QD growth gained from this work is then developed to controllably tune PbS QD shape from cubic to octahedral to hexapodal while maintaining QD size. At the following level of QD self-assembly (2), I show how QD size and shape dictate packing geometry in extended 2D arrays and how this packing can be controllably interrupted in mixed monolayers. I also study the role of ligand structure on the reorganization of QD arrays at a liquid-air interface and find that the specific packing defects in QD arrays vary

  2. Rotational spectra of rare isotopic species of fluoroiodomethane: determination of the equilibrium structure from rotational spectroscopy and quantum-chemical calculations.

    PubMed

    Puzzarini, Cristina; Cazzoli, Gabriele; López, Juan Carlos; Alonso, José Luis; Baldacci, Agostino; Baldan, Alessandro; Stopkowicz, Stella; Cheng, Lan; Gauss, Jürgen

    2012-07-14

    Supported by accurate quantum-chemical calculations, the rotational spectra of the mono- and bi-deuterated species of fluoroiodomethane, CHDFI and CD(2)FI, as well as of the (13)C-containing species, (13)CH(2)FI, were recorded for the first time. Three different spectrometers were employed, a Fourier-transform microwave spectrometer, a millimeter/submillimter-wave spectrometer, and a THz spectrometer, thus allowing to record a huge portion of the rotational spectrum, from 5 GHz up to 1.05 THz, and to accurately determine the ground-state rotational and centrifugal-distortion constants. Sub-Doppler measurements allowed to resolve the hyperfine structure of the rotational spectrum and to determine the complete iodine quadrupole-coupling tensor as well as the diagonal elements of the iodine spin-rotation tensor. The present investigation of rare isotopic species of CH(2)FI together with the results previously obtained for the main isotopologue [C. Puzzarini, G. Cazzoli, J. C. López, J. L. Alonso, A. Baldacci, A. Baldan, S. Stopkowicz, L. Cheng, and J. Gauss, J. Chem. Phys. 134, 174312 (2011); G. Cazzoli, A. Baldacci, A. Baldan, and C. Puzzarini, Mol. Phys. 109, 2245 (2011)] enabled us to derive a semi-experimental equilibrium structure for fluoroiodomethane by means of a least-squares fit procedure using the available experimental ground-state rotational constants together with computed vibrational corrections. Problems related to the missing isotopic substitution of fluorine and iodine were overcome thanks to the availability of an accurate theoretical equilibrium geometry (computed at the coupled-cluster singles and doubles level augmented by a perturbative treatment of triple excitations).

  3. Rotational spectra of rare isotopic species of fluoroiodomethane: Determination of the equilibrium structure from rotational spectroscopy and quantum-chemical calculations

    NASA Astrophysics Data System (ADS)

    Puzzarini, Cristina; Cazzoli, Gabriele; López, Juan Carlos; Alonso, José Luis; Baldacci, Agostino; Baldan, Alessandro; Stopkowicz, Stella; Cheng, Lan; Gauss, Jürgen

    2012-07-01

    Supported by accurate quantum-chemical calculations, the rotational spectra of the mono- and bi-deuterated species of fluoroiodomethane, CHDFI and CD2FI, as well as of the 13C-containing species, 13CH2FI, were recorded for the first time. Three different spectrometers were employed, a Fourier-transform microwave spectrometer, a millimeter/submillimter-wave spectrometer, and a THz spectrometer, thus allowing to record a huge portion of the rotational spectrum, from 5 GHz up to 1.05 THz, and to accurately determine the ground-state rotational and centrifugal-distortion constants. Sub-Doppler measurements allowed to resolve the hyperfine structure of the rotational spectrum and to determine the complete iodine quadrupole-coupling tensor as well as the diagonal elements of the iodine spin-rotation tensor. The present investigation of rare isotopic species of CH2FI together with the results previously obtained for the main isotopologue [C. Puzzarini, G. Cazzoli, J. C. López, J. L. Alonso, A. Baldacci, A. Baldan, S. Stopkowicz, L. Cheng, and J. Gauss, J. Chem. Phys. 134, 174312 (2011);, 10.1063/1.3583498 G. Cazzoli, A. Baldacci, A. Baldan, and C. Puzzarini, Mol. Phys. 109, 2245 (2011)], 10.1080/00268976.2011.609142 enabled us to derive a semi-experimental equilibrium structure for fluoroiodomethane by means of a least-squares fit procedure using the available experimental ground-state rotational constants together with computed vibrational corrections. Problems related to the missing isotopic substitution of fluorine and iodine were overcome thanks to the availability of an accurate theoretical equilibrium geometry (computed at the coupled-cluster singles and doubles level augmented by a perturbative treatment of triple excitations).

  4. High Color-Purity Green, Orange, and Red Light-Emitting Didoes Based on Chemically Functionalized Graphene Quantum Dots

    PubMed Central

    Kwon, Woosung; Kim, Young-Hoon; Kim, Ji-Hee; Lee, Taehyung; Do, Sungan; Park, Yoonsang; Jeong, Mun Seok; Lee, Tae-Woo; Rhee, Shi-Woo

    2016-01-01

    Chemically derived graphene quantum dots (GQDs) to date have showed very broad emission linewidth due to many kinds of chemical bondings with different energy levels, which significantly degrades the color purity and color tunability. Here, we show that use of aniline derivatives to chemically functionalize GQDs generates new extrinsic energy levels that lead to photoluminescence of very narrow linewidths. We use transient absorption and time-resolved photoluminescence spectroscopies to study the electronic structures and related electronic transitions of our GQDs, which reveals that their underlying carrier dynamics is strongly related to the chemical properties of aniline derivatives. Using these functionalized GQDs as lumophores, we fabricate light-emitting didoes (LEDs) that exhibit green, orange, and red electroluminescence that has high color purity. The maximum current efficiency of 3.47 cd A−1 and external quantum efficiency of 1.28% are recorded with our LEDs; these are the highest values ever reported for LEDs based on carbon-nanoparticle phosphors. This functionalization of GQDs with aniline derivatives represents a new method to fabricate LEDs that produce natural color. PMID:27048887

  5. High Color-Purity Green, Orange, and Red Light-Emitting Didoes Based on Chemically Functionalized Graphene Quantum Dots

    NASA Astrophysics Data System (ADS)

    Kwon, Woosung; Kim, Young-Hoon; Kim, Ji-Hee; Lee, Taehyung; Do, Sungan; Park, Yoonsang; Jeong, Mun Seok; Lee, Tae-Woo; Rhee, Shi-Woo

    2016-04-01

    Chemically derived graphene quantum dots (GQDs) to date have showed very broad emission linewidth due to many kinds of chemical bondings with different energy levels, which significantly degrades the color purity and color tunability. Here, we show that use of aniline derivatives to chemically functionalize GQDs generates new extrinsic energy levels that lead to photoluminescence of very narrow linewidths. We use transient absorption and time-resolved photoluminescence spectroscopies to study the electronic structures and related electronic transitions of our GQDs, which reveals that their underlying carrier dynamics is strongly related to the chemical properties of aniline derivatives. Using these functionalized GQDs as lumophores, we fabricate light-emitting didoes (LEDs) that exhibit green, orange, and red electroluminescence that has high color purity. The maximum current efficiency of 3.47 cd A‑1 and external quantum efficiency of 1.28% are recorded with our LEDs; these are the highest values ever reported for LEDs based on carbon-nanoparticle phosphors. This functionalization of GQDs with aniline derivatives represents a new method to fabricate LEDs that produce natural color.

  6. High Color-Purity Green, Orange, and Red Light-Emitting Didoes Based on Chemically Functionalized Graphene Quantum Dots

    NASA Astrophysics Data System (ADS)

    Kwon, Woosung; Kim, Young-Hoon; Kim, Ji-Hee; Lee, Taehyung; Do, Sungan; Park, Yoonsang; Jeong, Mun Seok; Lee, Tae-Woo; Rhee, Shi-Woo

    2016-04-01

    Chemically derived graphene quantum dots (GQDs) to date have showed very broad emission linewidth due to many kinds of chemical bondings with different energy levels, which significantly degrades the color purity and color tunability. Here, we show that use of aniline derivatives to chemically functionalize GQDs generates new extrinsic energy levels that lead to photoluminescence of very narrow linewidths. We use transient absorption and time-resolved photoluminescence spectroscopies to study the electronic structures and related electronic transitions of our GQDs, which reveals that their underlying carrier dynamics is strongly related to the chemical properties of aniline derivatives. Using these functionalized GQDs as lumophores, we fabricate light-emitting didoes (LEDs) that exhibit green, orange, and red electroluminescence that has high color purity. The maximum current efficiency of 3.47 cd A-1 and external quantum efficiency of 1.28% are recorded with our LEDs; these are the highest values ever reported for LEDs based on carbon-nanoparticle phosphors. This functionalization of GQDs with aniline derivatives represents a new method to fabricate LEDs that produce natural color.

  7. Enhanced Constraints for Accurate Lower Bounds on Many-Electron Quantum Energies from Variational Two-Electron Reduced Density Matrix Theory

    NASA Astrophysics Data System (ADS)

    Mazziotti, David A.

    2016-10-01

    A central challenge of physics is the computation of strongly correlated quantum systems. The past ten years have witnessed the development and application of the variational calculation of the two-electron reduced density matrix (2-RDM) without the wave function. In this Letter we present an orders-of-magnitude improvement in the accuracy of 2-RDM calculations without an increase in their computational cost. The advance is based on a low-rank, dual formulation of an important constraint on the 2-RDM, the T 2 condition. Calculations are presented for metallic chains and a cadmium-selenide dimer. The low-scaling T 2 condition will have significant applications in atomic and molecular, condensed-matter, and nuclear physics.

  8. Stabilization, Injection and Control of Quantum Cascade Lasers, and Their Appli-cation to Chemical Sensing in the Infrared

    SciTech Connect

    Taubman, Matthew S.; Myers, Tanya L.; Cannon, Bret D.; Williams, Richard M.

    2004-12-01

    Quantum cascade lasers (QCLs) are a relatively new type of semiconductor laser operating in the mid- to long-wave infrared. These monopolar multilayered quantum well structures can be fabricated to operate anywhere between 3.5 microns and 20 microns, which includes the molecular fingerprint region of the in-frared. This makes them an ideal choice for infrared chemical sensing, a topic of great interest at present. Frequency stabilization and injection locking increase the utility of QCLs. We present results of locking quantum cascade lasers to optical cavities, achieving relative linewidths down to 5.6 Hz. We report injec-tion locking of one distributed feedback grating QCL with light from a similar QCL, demonstrating capture ranges of up to ±500 MHz, and suppression of amplitude modulation by up to 49 dB. We also present various cavity-enhanced chemical sensors employing the frequency stabilization techniques developed, in-cluding the resonant sideband technique known as Nice-Ohms. Sensitivities of 9.7 x 10-11 cm-1 Hz-1/2 have been achieved in nitrous oxide.

  9. Isolation, characterization, spectroscopic properties and quantum chemical computations of an important phytoalexin resveratrol as antioxidant component from Vitis labrusca L. and their chemical compositions

    NASA Astrophysics Data System (ADS)

    Güder, Aytaç; Korkmaz, Halil; Gökce, Halil; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

    2014-12-01

    In this study, isolation and characterization of trans-resveratrol (RES) as an antioxidant compound were carried out from VLE, VLG and VLS. Furthermore, antioxidant activities were evaluated by using six different methods. Finally, total phenolic, flavonoid, ascorbic acid, anthocyanin, lycopene, β-carotene and vitamin E contents were carried out. In addition, the FT-IR, 13C and 1H NMR chemical shifts and UV-vis. spectra of trans-resveratrol were experimentally recorded. Quantum chemical computations such as the molecular geometry, vibrational frequencies, UV-vis. spectroscopic parameters, HOMOs-LUMOs energies, molecular electrostatic potential (MEP), natural bond orbitals (NBO) and nonlinear optics (NLO) properties of title molecule have been calculated by using DFT/B3PW91 method with 6-311++G(d,p) basis set in ground state for the first time. The obtained results show that the calculated spectroscopic data are in a good agreement with experimental data.

  10. Pure and N-substituted Small Cyclic Hydrocarbon Cations and Anions Synthesis in The Ionosphere of Titan: An Ab-Initio Quantum Chemical Perspective

    NASA Astrophysics Data System (ADS)

    Bera, P. P.

    2015-12-01

    The instruments on board the CASSINI spacecraft observed large carbonaceous molecules in the upper atmosphere of Titan. How these large polyatomic molecules are synthesized in such exotic conditions is, thus far, unknown. Molecular ions, including positive and negative ions, especially large anions, are in abundance in the ionosphere of Titan. Barrier-less ion-molecule interactions may play a major role ­- ions provide electrostatic steering force - in guiding molecules towards each other and initiating reactions. We study these condensation pathways to determine whether they are a viable means of forming large pure hydrocarbon molecules, and nitrogen-containing carbonaceous chains, stacks, and even cyclic compounds. We employ accurate quantum chemical methods to investigate the processes of growth, structures, nature of bonding, mechanisms, and spectroscopic properties of the ensuing ionic products after pairing small carbon, hydrogen, and nitrogen-containing molecules with major ions observed in the upper atmosphere of Titan, e.g. C2H5+ and HCNH+, apart from a whole host of small hydrocarbons. We also studied the ion-neutral association pathways involving pure-carbon molecules e.g. acetylene, ethylene and other hydrocarbons, and their dissociation fragments in a plasma discharge. We found the molecular building blocks of polycyclic aromatic hydrocarbons such as phenyl cations can form very easily by the combination of smaller hydrocarbons followed by hydrogen loss. We have investigated how nitrogen atoms are incorporated into the carbon ring during growth. Specifically, we explored the mechanisms by which the synthesis of pyrimidine will be feasible in the atmosphere of Titan in conjunction with ion-mobility experiments. Futher, we study the formation process of anions, and study their potential energy surfaces. We have used accurate ab initio coupled cluster theory, Møller-Plesset perturbation theory, density functional theory (DFT), and coupled cluster theory

  11. Experimental and quantum chemical studies of a novel synthetic prenylated chalcone

    PubMed Central

    2013-01-01

    Background Chalcones are ubiquitous natural compounds with a wide variety of reported biological activities, including antitumoral, antiviral and antimicrobial effects. Furthermore, chalcones are being studied for its potential use in organic electroluminescent devices; therefore the description of their spectroscopic properties is important to elucidate the structure of these molecules. One of the main techniques available for structure elucidation is the use of Nuclear Magnetic Resonance Spectroscopy (NMR). Accordingly, the prediction of the NMR spectra in this kind of molecules is necessary to gather information about the influence of substituents on their spectra. Results A novel substituted chalcone has been synthetized. In order to identify the functional groups present in the new synthesized compound and confirm its chemical structure, experimental and theoretical 1H-NMR and 13C-NMR spectra were analyzed. The theoretical molecular structure and NMR spectra were calculated at both the Hartree-Fock and Density Functional (meta: TPSS; hybrid: B3LYP and PBE1PBE; hybrid meta GGA: M05-2X and M06-2X) levels of theory in combination with a 6-311++G(d,p) basis set. The structural parameters showed that the best method for geometry optimization was DFT:M06-2X/6-311++G(d,p), whereas the calculated bond angles and bond distances match experimental values of similar chalcone derivatives. The NMR calculations were carried out using the Gauge-Independent Atomic Orbital (GIAO) formalism in a DFT:M06-2X/6-311++G(d,p) optimized geometry. Conclusion Considering all HF and DFT methods with GIAO calculations, TPSS and PBE1PBE were the most accurate methods used for calculation of 1H-NMR and 13C-NMR chemical shifts, which was almost similar to the B3LYP functional, followed in order by HF, M05-2X and M06-2X methods. All calculations were done using the Gaussian 09 software package. Theoretical calculations can be used to predict and confirm the structure of substituted chalcones

  12. Quantum chemical modelling of reactivity and selectivity of 1,2-dithiolanes towards retroviral and cellular zinc fingers

    NASA Astrophysics Data System (ADS)

    Topol, Igor A.; Nemukhin, Alexander V.; Burt, Stanley K.

    Interactions of 1,2-dithiolane species with zinc-containing sites, which mimic the zinc finger domains of retroviral and the cellular zinc finger proteins, have been investigated by quantum chemistry tools. According to the calculations, the immediate domains of zinc binding sites in the cellular and retroviral zinc fingers interact differently with such agents of the disulphide family. Thus, when approaching the model cellular-type domains, the molecules of 1,2-dithiolanes experience considerable potential barriers along the reaction path. However, these species react practically barrier-less with the model retroviral-type domains at the correlated DFT level. The results of the quantum chemical modelling provide firm support to the selectivity of 1,2-dithiolanes towards retroviral and cellular zinc fingers. This can be of great practical importance for the design of therapeutics that accomplish functional inactivation of the zinc fingers of the human immunodeficiency virus (HIV-1) retroviral type nucleocapsid protein NCp7.

  13. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1982-01-01

    Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

  14. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.

    PubMed

    Borbulevych, Oleg; Martin, Roger I; Tickle, Ian J; Westerhoff, Lance M

    2016-04-01

    Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  15. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

    PubMed Central

    Borbulevych, Oleg; Martin, Roger I.; Tickle, Ian J.; Westerhoff, Lance M.

    2016-01-01

    Gaining an understanding of the protein–ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  16. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

    PubMed

    Borbulevych, Oleg Y; Plumley, Joshua A; Martin, Roger I; Merz, Kenneth M; Westerhoff, Lance M

    2014-05-01

    Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

  17. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

    PubMed Central

    Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I.; Merz, Kenneth M.; Westerhoff, Lance M.

    2014-01-01

    Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography. PMID:24816093

  18. Refinement of the experimental energy levels of higher {sup 2}D Rydberg states of the lithium atom with very accurate quantum mechanical calculations

    SciTech Connect

    Sharkey, Keeper L.; Bubin, Sergiy; Adamowicz, Ludwik

    2011-05-21

    Very accurate variational non-relativistic calculations are performed for four higher Rydberg {sup 2}D states (1s{sup 2}nd{sup 1}, n= 8, ..., 11) of the lithium atom ({sup 7}Li). The wave functions of the states are expanded in terms of all-electron explicitly correlated Gaussian functions and finite nuclear mass is used. The exponential parameters of the Gaussians are optimized using the variational method with the aid of the analytical energy gradient determined with respect to those parameters. The results of the calculations allow for refining the experimental energy levels determined with respect to the {sup 2}S 1s{sup 2}2s{sup 1} ground state.

  19. Using multiple quantum coherence to increase the 15N resolution in a three-dimensional TROSY HNCO experiment for accurate PRE and RDC measurements.

    PubMed

    Hu, Kaifeng; Doucleff, Michaeleen; Clore, G Marius

    2009-10-01

    We present a new version of the 3D TROSY HNCO pulse scheme, referred to as HR-TROSY HNCO, with comparable resolution in the (15)N dimension to a 2D (1)H-(15)N HSQC experiment. In the conventional 3D TROSY HNCO, the constant time period (1/2J(NC) approximately 32 ms) severely limits the maximum resolution in the (15)N dimension. In the HR-TROSY HNCO experiment presented here, both constant time periods (approximately 32 ms each) for coherence forward and backward transfer between (15)N and (13)C' are utilized to double the (15)N evolution time. This leads to a dramatic enhancement in peak separation along the (15)N dimension, making the HR-TROSY HNCO an ideal pulse scheme for accurate paramagnetic relaxation enhancement and residual dipolar coupling measurements. PMID:19615926

  20. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

    PubMed

    Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

    2008-06-14

    Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

  1. First-principles quantum chemistry in the life sciences.

    PubMed

    van Mourik, Tanja

    2004-12-15

    The area of computational quantum chemistry, which applies the principles of quantum mechanics to molecular and condensed systems, has developed drastically over the last decades, due to both increased computer power and the efficient implementation of quantum chemical methods in readily available computer programs. Because of this, accurate computational techniques can now be applied to much larger systems than before, bringing the area of biochemistry within the scope of electronic-structure quantum chemical methods. The rapid pace of progress of quantum chemistry makes it a very exciting research field; calculations that are too computationally expensive today may be feasible in a few months' time! This article reviews the current application of 'first-principles' quantum chemistry in biochemical and life sciences research, and discusses its future potential. The current capability of first-principles quantum chemistry is illustrated in a brief examination of computational studies on neurotransmitters, helical peptides, and DNA complexes.

  2. The structure and photochemical transformation of cyclopropylacetylene radical cation as revealed by matrix EPR and quantum chemical study

    NASA Astrophysics Data System (ADS)

    Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

    2012-05-01

    The primary radical cation of cyclopropylacetylene was first characterized by EPR spectroscopy in low-temperature freon matrices. The assignment was confirmed by specific deuteration and quantum-chemical calculations at PBE0 and CCSD(T) levels. Photolysis with visible light led to irreversible transformation of the initial species to a ring-open structure. Detailed computational analysis of energy and magnetic resonance parameters of possible reaction products justified formation of pent-3-en-1-yne radical cation (presumably, a (Z)-isomer). This conclusion was also supported by the effect of specific deuteration.

  3. Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium

    PubMed Central

    Filho, Manoel A. M.; Dutra, José Diogo L.; Rocha, Gerd B.; Simas, Alfredo M.

    2016-01-01

    The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications. PMID:27223475

  4. Quantum chemical approach for condensed-phase thermochemistry (II): Applications to formation and combustion reactions of liquid organic molecules

    NASA Astrophysics Data System (ADS)

    Ishikawa, Atsushi; Nakai, Hiromi

    2015-03-01

    The harmonic solvation model (HSM), which was recently developed for evaluating condensed-phase thermodynamics by quantum chemical calculations (Nakai and Ishikawa, 2014), was applied to formation and combustion reactions of simple organic molecules. The conventional ideal gas model (IGM) considerably overestimated the entropies of the liquid molecules. The HSM could significantly improve this overestimation; mean absolute deviations for the Gibbs energies of the formation and combustion reactions were (49.6, 26.7) for the IGM and (9.7, 5.4) for the HSM in kJ/mol.

  5. Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium.

    PubMed

    Filho, Manoel A M; Dutra, José Diogo L; Rocha, Gerd B; Simas, Alfredo M; Freire, Ricardo O

    2016-01-01

    The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications.

  6. Parameters for the RM1 Quantum Chemical Calculation of Complexes of the Trications of Thulium, Ytterbium and Lutetium.

    PubMed

    Filho, Manoel A M; Dutra, José Diogo L; Rocha, Gerd B; Simas, Alfredo M; Freire, Ricardo O

    2016-01-01

    The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications. PMID:27223475

  7. Prediction of {sup 2}D Rydberg energy levels of {sup 6}Li and {sup 7}Li based on very accurate quantum mechanical calculations performed with explicitly correlated Gaussian functions

    SciTech Connect

    Bubin, Sergiy; Sharkey, Keeper L.; Adamowicz, Ludwik

    2013-04-28

    Very accurate variational nonrelativistic finite-nuclear-mass calculations employing all-electron explicitly correlated Gaussian basis functions are carried out for six Rydberg {sup 2}D states (1s{sup 2}nd, n= 6, Horizontal-Ellipsis , 11) of the {sup 7}Li and {sup 6}Li isotopes. The exponential parameters of the Gaussian functions are optimized using the variational method with the aid of the analytical energy gradient determined with respect to these parameters. The experimental results for the lower states (n= 3, Horizontal-Ellipsis , 6) and the calculated results for the higher states (n= 7, Horizontal-Ellipsis , 11) fitted with quantum-defect-like formulas are used to predict the energies of {sup 2}D 1s{sup 2}nd states for {sup 7}Li and {sup 6}Li with n up to 30.

  8. Micromechanical measurement of beating patterns in the quantum oscillatory chemical potential of InGaAs quantum wells due to spin-orbit coupling

    SciTech Connect

    Herzog, Florian Wilde, Marc A.; Heyn, Christian; Hardtdegen, Hilde; Schäpers, Thomas; Grundler, Dirk

    2015-08-31

    The quantum oscillatory magnetization M(B) and chemical potential μ(B) of a two-dimensional (2D) electron system provide important and complementary information about its ground state energy at low temperature T. We developed a technique that provides both quantities in the same cool-down process via a decoupled static operation and resonant excitation of a micromechanical cantilever. On InGaAs/InP heterostructures, we observed beating patterns in both M(B) and μ(B) attributed to spin-orbit interaction. A significantly enhanced sensitivity in μ enabled us to extract Rashba and Dresselhaus parameters with high accuracy. The technique is powerful for detailed investigations on the electronic properties of 2D materials.

  9. Quantum chemical study of the mechanism of action of vitamin K epoxide reductase (VKOR)

    NASA Astrophysics Data System (ADS)

    Deerfield, David, II; Davis, Charles H.; Wymore, Troy; Stafford, Darrel W.; Pedersen, Lee G.

    Possible model, but simplistic, mechanisms for the action of vitamin K epoxide reductase (VKOR) are investigated with quantum mechanical methods (B3LYP/6-311G**). The geometries of proposed model intermediates in the mechanisms are energy optimized. Finally, the energetics of the proposed (pseudo-enzymatic) pathways are compared. We find that the several pathways are all energetically feasible. These results will be useful for designing quantum mechanical/molecular mechanical method (QM/MM) studies of the enzymatic pathway once three-dimensional structural data are determined and available for VKOR.

  10. Unification of ground-state aromaticity criteria - structure, electron delocalization, and energy - in light of the quantum chemical topology.

    PubMed

    Badri, Zahra; Foroutan-Nejad, Cina

    2016-04-28

    In the present account we investigate a theoretical link between the bond length, electron sharing, and bond energy within the context of quantum chemical topology theories. The aromatic stabilization energy, ASE, was estimated from this theoretical link without using isodesmic reactions for the first time. The ASE values obtained from our method show a meaningful correlation with the number of electrons contributing to the aromaticity. This theoretical link demonstrates that structural, electronic, and energetic criteria of aromaticity - ground-state aromaticity - belong to the same class and guarantees that they assess the same property as aromaticity. Theory suggests that interatomic exchange-correlation potential, obtained from the theory of Interacting Quantum Atoms (IQA), is linearly connected to the delocalization index of Quantum Theory of Atoms in Molecules (QTAIM) and the bond length through a first order approximation. Our study shows that the relationship between energy, structure and electron sharing marginally deviates from the ideal linear form expected from the first order approximation. The observed deviation from linearity was attributed to a different contribution of exchange-correlation to the bond energy for the σ- and π-frameworks. Finally, we proposed two-dimensional energy-structure-based aromaticity indices in analogy to the electron sharing indices of aromaticity. PMID:26678719

  11. Unification of ground-state aromaticity criteria - structure, electron delocalization, and energy - in light of the quantum chemical topology.

    PubMed

    Badri, Zahra; Foroutan-Nejad, Cina

    2016-04-28

    In the present account we investigate a theoretical link between the bond length, electron sharing, and bond energy within the context of quantum chemical topology theories. The aromatic stabilization energy, ASE, was estimated from this theoretical link without using isodesmic reactions for the first time. The ASE values obtained from our method show a meaningful correlation with the number of electrons contributing to the aromaticity. This theoretical link demonstrates that structural, electronic, and energetic criteria of aromaticity - ground-state aromaticity - belong to the same class and guarantees that they assess the same property as aromaticity. Theory suggests that interatomic exchange-correlation potential, obtained from the theory of Interacting Quantum Atoms (IQA), is linearly connected to the delocalization index of Quantum Theory of Atoms in Molecules (QTAIM) and the bond length through a first order approximation. Our study shows that the relationship between energy, structure and electron sharing marginally deviates from the ideal linear form expected from the first order approximation. The observed deviation from linearity was attributed to a different contribution of exchange-correlation to the bond energy for the σ- and π-frameworks. Finally, we proposed two-dimensional energy-structure-based aromaticity indices in analogy to the electron sharing indices of aromaticity.

  12. Comparative electron paramagnetic resonance investigation of reduced graphene oxide and carbon nanotubes with different chemical functionalities for quantum dot attachment

    NASA Astrophysics Data System (ADS)

    Pham, Chuyen V.; Krueger, Michael; Eck, Michael; Weber, Stefan; Erdem, Emre

    2014-03-01

    Electron paramagnetic resonance (EPR) spectroscopy has been applied to different chemically treated reduced graphene oxide (rGO) and multiwalled carbon nanotubes (CNTs). A narrow EPR signal is visible at g = 2.0029 in both GO and CNT-Oxide from carbon-related dangling bonds. EPR signals became broader and of lower intensity after oxygen-containing functionalities were reduced and partially transformed into thiol groups to obtain thiol-functionalized reduced GO (TrGO) and thiol-functionalized CNT (CNT-SH), respectively. Additionally, EPR investigation of CdSe quantum dot-TrGO hybrid material reveals complete quenching of the TrGO EPR signal due to direct chemical attachment and electronic coupling. Our work confirms that EPR is a suitable tool to detect spin density changes in different functionalized nanocarbon materials and can contribute to improved understanding of electronic coupling effects in nanocarbon-nanoparticle hybrid nano-composites promising for various electronic and optoelectronic applications.

  13. Use of external cavity quantum cascade laser compliance voltage in real-time trace gas sensing of multiple chemicals

    NASA Astrophysics Data System (ADS)

    Phillips, Mark C.; Taubman, Matthew S.; Kriesel, Jason

    2015-01-01

    We describe a prototype trace gas sensor designed for real-time detection of multiple chemicals. The sensor uses an external cavity quantum cascade laser (ECQCL) swept over its tuning range of 940-1075 cm-1 (9.30-10.7 μm) at a 10 Hz repetition rate. The sensor was designed for operation in multiple modes, including gas sensing within a multi-pass Heriott cell and intracavity absorption sensing using the ECQCL compliance voltage. In addition, the ECQCL compliance voltage was used to reduce effects of long-term drifts in the ECQCL output power. The sensor was characterized for noise, drift, and detection of chemicals including ammonia, methanol, ethanol, isopropanol, Freon- 134a, Freon-152a, and diisopropyl methylphosphonate (DIMP). We also present use of the sensor for mobile detection of ammonia downwind of cattle facilities, in which concentrations were recorded at 1-s intervals.

  14. Quantum Chemical Studies on the Prediction of Structures, Charge Distributions and Vibrational Spectra of Some Ni(II), Zn(II), and Cd(II) Iodide Complexes

    NASA Astrophysics Data System (ADS)

    Bardakci, Tayyibe; Kumru, Mustafa; Altun, Ahmet

    2016-06-01

    Transition metal complexes play an important role in coordination chemistry as well as in the formation of metal-based drugs. In order to obtain accurate results for studying these type of complexes quantum chemical studies are performed and especially density functional theory (DFT) has become a promising choice. This talk represents molecular structures, charge distributions and vibrational analysis of Ni(II), Zn(II), and Cd(II) iodide complexes of p-toluidine and m-toluidine by means of DFT. Stable structures of the ligands and the related complexes have been obtained in the gas phase at B3LYP/def2-TZVP level and calculations predict Ni(II) complexes as distorted polymeric octahedral whereas Zn(II) and Cd(II) complexes as distorted tetrahedral geometries. Charge distribution analysis have been performed by means of Mulliken, NBO and APT methods and physically most meaningful method for our compounds is explained. Vibrational spectra of the title compounds are computed from the optimized geometries and theoretical frequencies are compared with the previously obtained experimental data. Since coordination occurs via nitrogen atoms of the free ligands, N-H stretching bands of the ligands are shifted towards lower wavenumbers in the complexes whereas NH_2 wagging and twisting vibrations are shifted towards higher wavenumbers.

  15. Structure of the antiviral stavudine using quantum chemical methods: Complete conformational space analysis, 3D potential energy surfaces and solid state simulations

    NASA Astrophysics Data System (ADS)

    Alcolea Palafox, M.; Iza, N.

    2012-11-01

    The molecular structure and energy of the anti-HIV, 2',3'-didehydro-3'-deoxythymidine (D4T, stavudine or Zerit) nucleoside analogue was determined by using MP2, B3LYP and B971 quantum chemical methods. The global minimum was determined through 3D potential energy surfaces (PES). These surfaces were built by rotation of the exocyclic χ, γ and β torsional angles, in steps of 20°, and full optimization of the remaining parameters. As consequence 5832 geometries were final optimized. The search located 25 local minimum, 4 of which are by MP2 within a 2 kcal/mol electronic energy range of the global minimum. The whole conformational parameters as well as P, νmax were analyzed in all the stable conformers. The global minimum by MP2 corresponds to the calculated values of the exocyclic torsional angles: χ = -103.6°, β = 63.8° and γ = 60.6°. The results obtained are in accordance to those found in thymidine and in related anti-HIV nucleoside analogues. The effect of hydration on the two most stable conformers is analyzed by continuous and discrete models up to 20 water molecules. The solid state was also simulated. The dimer forms found in the crystal unit cell were accurately determined and they are in accordance to the X-ray data.

  16. Evidence for excited-state intramolecular proton transfer in 4-chlorosalicylic acid from combined experimental and computational studies: Quantum chemical treatment of the intramolecular hydrogen bonding interaction

    NASA Astrophysics Data System (ADS)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2012-07-01

    The photophysical study of a pharmaceutically important chlorine substituted derivative of salicylic acid viz., 4-chlorosalicylic acid (4ClSA) has been carried out by steady-state absorption, emission and time-resolved emission spectroscopy. A large Stokes shifted emission band with negligible solvent polarity dependence marks the spectroscopic signature of excited-state intramolecular proton transfer (ESIPT) reaction in 4ClSA. Theoretical calculation by ab initio and Density Functional Theory methods yields results consistent with experimental findings. Theoretical potential energy surfaces predict the occurrence of proton transfer in S1-state. Geometrical and energetic criteria, Atoms-In-Molecule topological parameters, Natural Bond Orbital population analysis have been exploited to evaluate the intramolecular hydrogen bond (IMHB) interaction and to explore its directional nature. The inter-correlation between aromaticity and resonance assisted H-bond is also discussed in this context. Our results unveil that the quantum chemical treatment is a more accurate tool to assess hydrogen bonding interaction in comparison to geometrical criteria.

  17. Chemical Reaction CO+OH(•) → CO2+H(•) Autocatalyzed by Carbon Dioxide: Quantum Chemical Study of the Potential Energy Surfaces.

    PubMed

    Masunov, Artëm E; Wait, Elizabeth; Vasu, Subith S

    2016-08-01

    The supercritical carbon dioxide medium, used to increase efficiency in oxy combustion fossil energy technology, may drastically alter both rates and mechanisms of chemical reactions. Here we investigate potential energy surface of the second most important combustion reaction with quantum chemistry methods. Two types of effects are reported: formation of the covalent intermediates and formation of van der Waals complexes by spectator CO2 molecule. While spectator molecule alter the activation barrier only slightly, the covalent bonding opens a new reaction pathway. The mechanism includes sequential covalent binding of CO2 to OH radical and CO molecule, hydrogen transfer from oxygen to carbon atoms, and CH bond dissociation. This reduces the activation barrier by 11 kcal/mol at the rate-determining step and is expected to accelerate the reaction rate. The finding of predicted catalytic effect is expected to play an important role not only in combustion but also in a broad array of chemical processes taking place in supercritical CO2 medium. It may open a new venue for controlling reaction rates for chemical manufacturing. PMID:27351778

  18. Chemical Reaction CO+OH(•) → CO2+H(•) Autocatalyzed by Carbon Dioxide: Quantum Chemical Study of the Potential Energy Surfaces.

    PubMed

    Masunov, Artëm E; Wait, Elizabeth; Vasu, Subith S

    2016-08-01

    The supercritical carbon dioxide medium, used to increase efficiency in oxy combustion fossil energy technology, may drastically alter both rates and mechanisms of chemical reactions. Here we investigate potential energy surface of the second most important combustion reaction with quantum chemistry methods. Two types of effects are reported: formation of the covalent intermediates and formation of van der Waals complexes by spectator CO2 molecule. While spectator molecule alter the activation barrier only slightly, the covalent bonding opens a new reaction pathway. The mechanism includes sequential covalent binding of CO2 to OH radical and CO molecule, hydrogen transfer from oxygen to carbon atoms, and CH bond dissociation. This reduces the activation barrier by 11 kcal/mol at the rate-determining step and is expected to accelerate the reaction rate. The finding of predicted catalytic effect is expected to play an important role not only in combustion but also in a broad array of chemical processes taking place in supercritical CO2 medium. It may open a new venue for controlling reaction rates for chemical manufacturing.

  19. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

    PubMed

    Ditzler, Mark A; Otyepka, Michal; Sponer, Jirì; Walter, Nils G

    2010-01-19

    Structure and dynamics are both critical to RNA's vital functions in biology. Numerous techniques can elucidate the structural dynamics of RNA, but computational approaches based on experimental data arguably hold the promise of providing the most detail. In this Account, we highlight areas wherein molecular dynamics (MD) and quantum mechanical (QM) techniques are applied to RNA, particularly in relation to complementary experimental studies. We have expanded on atomic-resolution crystal structures of RNAs in functionally relevant states by applying explicit solvent MD simulations to explore their dynamics and conformational changes on the submicrosecond time scale. MD relies on simplified atomistic, pairwise additive interaction potentials (force fields). Because of limited sampling, due to the finite accessible simulation time scale and the approximated force field, high-quality starting structures are required. Despite their imperfection, we find that currently available force fields empower MD to provide meaningful and predictive information on RNA dynamics around a crystallographically defined energy minimum. The performance of force fields can be estimated by precise QM calculations on small model systems. Such calculations agree reasonably well with the Cornell et al. AMBER force field, particularly for stacking and hydrogen-bonding interactions. A final verification of any force field is accomplished by simulations of complex nucleic acid structures. The performance of the Cornell et al. AMBER force field generally corresponds well with and augments experimental data, but one notable exception could be the capping loops of double-helical stems. In addition, the performance of pairwise additive force fields is obviously unsatisfactory for inclusion of divalent cations, because their interactions lead to major polarization and charge-transfer effects neglected by the force field. Neglect of polarization also limits, albeit to a lesser extent, the description

  20. Chemical Principles Revisited: Perspectives on the Uncertainty Principle and Quantum Reality.

    ERIC Educational Resources Information Center

    Bartell, Lawrence S.

    1985-01-01

    Explicates an approach that not only makes the uncertainty seem more useful to introductory students but also helps convey the real meaning of the term "uncertainty." General topic areas addressed include probability amplitudes, rationale behind the uncertainty principle, applications of uncertainty relations, and quantum processes. (JN)

  1. Wet chemical synthesis of quantum confined nanostructured tin oxide thin films by successive ionic layer adsorption and reaction technique

    SciTech Connect

    Murali, K.V.; Ragina, A.J.; Preetha, K.C.; Deepa, K.; Remadevi, T.L.

    2013-09-01

    Graphical abstract: - Highlights: • Quantum confined SnO{sub 2} thin films were synthesized at 80 °C by SILAR technique. • Film formation mechanism is discussed. • Films with snow like crystallite morphology offer high specific surface area. • The blue-shifted value of band gap confirmed the quantum confinement effect. • Present synthesis has advantages – low cost, low temperature and green friendly. - Abstract: Quantum confined nanostructured SnO{sub 2} thin films were synthesized at 353 K using ammonium chloride (NH{sub 4}Cl) and other chemicals by successive ionic layer adsorption and reaction technique. Film formation mechanism is discussed. Structural, morphological, optical and electrical properties were investigated and compared with the as-grown and annealed films fabricated without NH{sub 4}Cl solution. SnO{sub 2} films were polycrystalline with crystallites of tetragonal structure with grain sizes lie in the 5–8 nm range. Films with snow like crystallite morphology offer high specific surface area. The blue-shifted value of band gap of as-grown films confirmed the quantum confinement effect of grains. Refractive index of the films lies in the 2.1–2.3 range. Films prepared with NH{sub 4}Cl exhibit relatively lower resistivity of the order of 10{sup 0}–10{sup −1} Ω cm. The present synthesis has advantages such as low cost, low temperature and green friendly, which yields small particle size, large surface–volume ratio, and high crystallinity SnO{sub 2} films.

  2. Synthesis, microwave spectrum, quantum chemical calculations, and conformational composition of the novel compound cyclopropylethylidynephosphine (C₃H₅CH₂C≡P).

    PubMed

    Samdal, Svein; Møllendal, Harald; Guillemin, Jean-Claude

    2014-10-30

    The synthesis of the novel compound cyclopropylethylidynephosphine (C3H5CH2C≡P) and its microwave spectrum are reported together with quantum chemical calculations. The spectrum, which reveals the existence of two conformers, has been recorded in the 38-109 GHz spectral range at room temperature. The H-C-CH2-C chain of atoms is synclinal in one rotamer denoted sc, and antiperiplanar in the second conformer called ap. The spectra of the ground vibrational state and two vibrationally excited states were assigned for each rotamer. The vibrational frequencies of these excited states were determined by relative intensity measurements. Relative intensity measurements were also conducted to determine the energy difference between ap and sc. The latter conformer was found to be the lower-energy form and E(ap) - E(sc) was determined to be 0.9(4) kJ/mol. The microwave study has been augmented by quantum chemical calculations at the CCSD/cc-pVQZ and MP2/cc-pVTZ levels of theory. The CCSD predictions were generally in good agreement with experiment, while somewhat mixed results were obtained in the MP2 calculations.

  3. Prediction of Radical Scavenging Activities of Anthocyanins Applying Adaptive Neuro-Fuzzy Inference System (ANFIS) with Quantum Chemical Descriptors

    PubMed Central

    Jhin, Changho; Hwang, Keum Taek

    2014-01-01

    Radical scavenging activity of anthocyanins is well known, but only a few studies have been conducted by quantum chemical approach. The adaptive neuro-fuzzy inference system (ANFIS) is an effective technique for solving problems with uncertainty. The purpose of this study was to construct and evaluate quantitative structure-activity relationship (QSAR) models for predicting radical scavenging activities of anthocyanins with good prediction efficiency. ANFIS-applied QSAR models were developed by using quantum chemical descriptors of anthocyanins calculated by semi-empirical PM6 and PM7 methods. Electron affinity (A) and electronegativity (χ) of flavylium cation, and ionization potential (I) of quinoidal base were significantly correlated with radical scavenging activities of anthocyanins. These descriptors were used as independent variables for QSAR models. ANFIS models with two triangular-shaped input fuzzy functions for each independent variable were constructed and optimized by 100 learning epochs. The constructed models using descriptors calculated by both PM6 and PM7 had good prediction efficiency with Q-square of 0.82 and 0.86, respectively. PMID:25153627

  4. Prediction of radical scavenging activities of anthocyanins applying adaptive neuro-fuzzy inference system (ANFIS) with quantum chemical descriptors.

    PubMed

    Jhin, Changho; Hwang, Keum Taek

    2014-01-01

    Radical scavenging activity of anthocyanins is well known, but only a few studies have been conducted by quantum chemical approach. The adaptive neuro-fuzzy inference system (ANFIS) is an effective technique for solving problems with uncertainty. The purpose of this study was to construct and evaluate quantitative structure-activity relationship (QSAR) models for predicting radical scavenging activities of anthocyanins with good prediction efficiency. ANFIS-applied QSAR models were developed by using quantum chemical descriptors of anthocyanins calculated by semi-empirical PM6 and PM7 methods. Electron affinity (A) and electronegativity (χ) of flavylium cation, and ionization potential (I) of quinoidal base were significantly correlated with radical scavenging activities of anthocyanins. These descriptors were used as independent variables for QSAR models. ANFIS models with two triangular-shaped input fuzzy functions for each independent variable were constructed and optimized by 100 learning epochs. The constructed models using descriptors calculated by both PM6 and PM7 had good prediction efficiency with Q-square of 0.82 and 0.86, respectively. PMID:25153627

  5. Computational simulation of the effect of quantum chemical parameters on the molecular docking of HMG-CoA reductase drugs

    NASA Astrophysics Data System (ADS)

    Atlam, Faten M.; Awad, Mohamed K.; El-Bastawissy, Eman A.

    2014-10-01

    Density functional theory (B3LYP-6-31G(d)) was performed to study the effect of molecular and electronic structures, of 2-cyclopropyl-4-thiophenyl-quinoline mevalonolactones as potential hypocholesterolemic inhibitors, on their biological activities and discuss the correlation between the inhibition efficiency and quantum chemical parameters. Molecular docking was performed to investigate the mode of interactions between the investigated inhibitors and the active sites of the target Hydroxymethylglutaryl-Coenzyme A(HMG-CoA) reductase. The results could suggest further structural modifications to discover more potent and selective HMG-CoA reductase inhibitors. The catalytic active sites of HMGR have a positive electrostatic potential which is complemented with a negative electrostatic potential of the investigated drugs to form a stabilized complex. The presence of lipophobic groups, such as quinoline nucleus, cyclopropyl and substituted thiophenyl groups as well as a lactone moiety, is important for binding to the active sites. A good correlation between the experimental and theoretical data confirms that the quantum chemical methods and molecular docking studies are successful tools for enriching screening experiments aimed at the discovery of novel bioactive compounds.

  6. Stabilization, injection and control of quantum cascade lasers, and their application to chemical sensing in the infrared.

    PubMed

    Taubman, Matthew S; Myers, Tanya L; Cannon, Bret D; Williams, Richard M

    2004-12-01

    Quantum cascade lasers (QCLs) are a relatively new type of semiconductor laser operating in the mid- to long-wave infrared. These monopolar multilayered quantum well structures can be fabricated to operate anywhere between 3.5 and 20 microm, which includes the molecular fingerprint region of the infrared. This makes them an ideal choice for infrared chemical sensing, a topic of great interest at present. Frequency stabilization and injection locking increase the utility of QCLs. We present results of locking QCLs to optical cavities, achieving relative linewidths down to 5.6 Hz. We report injection locking of one distributed feedback grating QCL with light from a similar QCL, demonstrating capture ranges of up to +/-500 MHz, and suppression of amplitude modulation by up to 49 dB. We also present various cavity-enhanced chemical sensors employing the frequency stabilization techniques developed, including the resonant sideband technique known as NICE-OHMS. Sensitivities of 9.7 x 10(-11) cm(-1) Hz(-1/2) have been achieved in pure nitrous oxide.

  7. Spectroscopic and quantum chemical correlation for structural evaluation, chemical reactivity and non-linear optical property investigation of two chalcone having pyrrole moiety: A comparative study

    NASA Astrophysics Data System (ADS)

    Singh, R. N.; Rawat, Poonam; Baboo, Vikas; Kumar, Yashvinder

    2015-04-01

    As part of study of pyrrole-chalcone, ethyl 4-[3-(4-chloro-phenyl)-acryloyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate (ECADPC) and ethyl 3,5-dimethyl-4-[3-(3-nitro-phenyl)-acryloyl]-1H-pyrrole-2-carboxylate (EDNAPC) have been synthesized by Claisen-Schmidt condensation using chloro- and nitro- substituted aromatic aldehyde and ethyl 3,5-dimetyl-4-acetyl-1H-pyrrole-2-carboxylate. The products were characterized by 1H NMR, UV-Visible, FT-IR spectroscopic methods and Quantum chemical calculations. Conformational analysis, normal mode frequencies and corresponding vibrational assignments based on potential energy distribution study revealed that ECADPC and EDNAPC exist in dimer form in solid state. 'Quantum theory of Atoms in molecules' (QTAIM) analysis has been performed to know the strength of intra- and intermolecular interactions. The UV-Visible spectra study reveals that the compounds are almost transparent in the visible region. Angular distribution of the probability density for population conformational analysis of ECADPC and EDNAPC are determined by analysis of the potential energy surface (PES). The calculated static first hyperpolarizability (β0) value for monomers of ECADPC and EDNAPC are 17.078 × 10-30 and 2.344 × 10-30 esu respectively, infers ECADPC to be more suitable for non-linear optical (NLO) response than EDNAPC. The electronic descriptors analysis predicts the nature of local reactive sites within the molecule.

  8. Synthesis, conformational, spectroscopic and chemical reactivity analysis of 2-cyano-3-(1H-pyrrol-2-yl)acrylohydrazide using experimental and quantum chemical approaches

    NASA Astrophysics Data System (ADS)

    Rawat, Poonam; Singh, R. N.

    2015-02-01

    This paper describes the synthesis, spectroscopic (1H and 13C NMR, UV-Visible, FT-IR and ESI Mass), conformational analysis, chemical reactivity and non-linear optical (NLO) properties of newly synthesized pyrrole derivative 2-cyano-3-(1H-pyrrol-2-yl)acrylohydrazide (2CPA) C8H8N4O using experimental and quantum chemical techniques. The presence of signal at δ 8.010 ppm due to vinyl proton as well as NH and NH2 protons signals at 11.054 and 2.499 ppm in experimental 1H NMR spectrum indicate that 2CPA contain sbnd CHdbnd CCNsbnd and sbnd NHsbnd NH2 frame. The combined experimental and theoretical symmetric (3194 cm-1) and asymmetric (3221 cm-1) stretching wavenumber analysis confirms free NH2 group in the solid phase FT-IR spectrum of the synthesized compound. The interaction energies of dimer formation using density functional theory (DFT) and Quantum theory of Atoms in Molecules (QTAIM) calculations are found to be 20.210, 19.683 kcal/mol, respectively. The maximum values of the electrophilic reactivity descriptors at C6 indicate that this site is more prone to nucleophilic attack and favoring the formation of heterocyclic derivatives. A natural bond orbital (NBOs) analysis has been carried out to investigate intramolecular charge transfer, conjugative and hyperconjugative interactions within molecule. The calculated first hyperpolarizability (β0) of 2CPA, indicates that investigated molecule will show non-linear optical response and might be used as non-linear optical (NLO) material.

  9. The chemical fate of the Cd/Se/Te-based quantum dot 705 in the biological system: toxicity implications

    NASA Astrophysics Data System (ADS)

    Lin, Chia-Hua; Chang, Louis W.; Chang, Han; Yang, Mo-Hsiung; Yang, Chung-Shi; Lai, Wan-Hau; Chang, Wan-Hsuan; Lin, Pinpin

    2009-05-01

    QD705 is a cadmium/selenium/tellurium (Cd/Se/Te)-based quantum dot with good potential for biomedical applications. Although the biological fate of QD705 is established, its chemical fate in the biological system is still unknown. Since the chemical nature of Cd in QD705 (either stays as bounded Cd or becomes free Cd) is closely related to the toxicity of this nanocrystal, information on its chemical fate is critically needed. In this study we investigated the chemical fate of QD705 in the kidneys of mice. We used the molar ratio of Cd and Te (increased Cd/Te ratio signifies increased Cd release from QD705) and the induction of tissue metallothionein (MT) as markers for elevated free Cd in tissues. Our study indicated that 100% of QD705 (measured as Cd) was still retained in the body 16 weeks after exposure, with significant time redistribution to the kidneys. Furthermore, there were an elevation in both the molar Cd/Te ratio and MT-1 expression in the kidneys, suggesting that free Cd was released from QD705. Thus QD705 is not as stable or biologically inert as many may have once believed. Our study demonstrated that free Cd indeed can be released from QD705 in the kidneys and increases the risk of renal toxicity.

  10. Reliable but Timesaving: In Search of an Efficient Quantum-chemical Method for the Description of Functional Fullerenes.

    PubMed

    Reis, H; Rasulev, B; Papadopoulos, M G; Leszczynski, J

    2015-01-01

    Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C60 and C70 fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans' theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives. PMID:25961522

  11. Reliable but Timesaving: In Search of an Efficient Quantum-chemical Method for the Description of Functional Fullerenes.

    PubMed

    Reis, H; Rasulev, B; Papadopoulos, M G; Leszczynski, J

    2015-01-01

    Fullerene and its derivatives are currently one of the most intensively investigated species in the area of nanomedicine and nanochemistry. Various unique properties of fullerenes are responsible for their wide range applications in industry, biology and medicine. A large pool of functionalized C60 and C70 fullerenes is investigated theoretically at different levels of quantum-mechanical theory. The semiempirial PM6 method, density functional theory with the B3LYP functional, and correlated ab initio MP2 method are employed to compute the optimized structures, and an array of properties for the considered species. In addition to the calculations for isolated molecules, the results of solution calculations are also reported at the DFT level, using the polarizable continuum model (PCM). Ionization potentials (IPs) and electron affinities (EAs) are computed by means of Koopmans' theorem as well as with the more accurate but computationally expensive ΔSCF method. Both procedures yield comparable values, while comparison of IPs and EAs computed with different quantum-mechanical methods shows surprisingly large differences. Harmonic vibrational frequencies are computed at the PM6 and B3LYP levels of theory and compared with each other. A possible application of the frequencies as 3D descriptors in the EVA (EigenVAlues) method is shown. All the computed data are made available, and may be used to replace experimental data in routine applications where large amounts of data are required, e.g. in structure-activity relationship studies of the toxicity of fullerene derivatives.

  12. PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

    PubMed Central

    Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  13. The Interplay of Quantum Confinement and Hydrogenation in Amorphous Silicon Quantum Dots.

    PubMed

    Askari, Sadegh; Svrcek, Vladmir; Maguire, Paul; Mariotti, Davide

    2015-12-22

    Hydrogenation in amorphous silicon quantum dots (QDs) has a dramatic impact on the corresponding optical properties and band energy structure, leading to a quantum-confined composite material with unique characteristics. The synthesis of a-Si:H QDs is demonstrated with an atmospheric-pressure plasma process, which allows for accurate control of a highly chemically reactive non-equilibrium environment with temperatures well below the crystallization temperature of Si QDs.

  14. Molecular dispersion spectroscopy for chemical sensing using chirped mid-infrared quantum cascade laser.

    PubMed

    Wysocki, Gerard; Weidmann, Damien

    2010-12-01

    A spectroscopic method of molecular detection based on dispersion measurements using a frequency-chirped laser source is presented. An infrared quantum cascade laser emitting around 1912 cm(-1) is used as a tunable spectroscopic source to measure dispersion that occurs in the vicinity of molecular ro-vibrational transitions. The sample under study is a mixture of nitric oxide in dry nitrogen. Two experimental configurations based on a coherent detection scheme are investigated and discussed. The theoretical models, which describe the observed spectral signals, are developed and verified experimentally. The method is particularly relevant to optical sensing based on mid-infrared quantum cascade lasers as the high chirp rates available with those sources can significantly enhance the magnitude of the measured dispersion signals. The method relies on heterodyne beatnote frequency measurements and shows high immunity to variations in the optical power received by the photodetector.

  15. Synthesis of copper quantum dots by chemical reduction method and tailoring of its band gap

    NASA Astrophysics Data System (ADS)

    Prabhash, P. G.; Nair, Swapna S.

    2016-05-01

    Metallic copper nano particles are synthesized with citric acid and CTAB (cetyltrimethylammonium bromide) as surfactant and chlorides as precursors. The particle size and surface morphology are analyzed by High Resolution Transmission Electron Microscopy. The average size of the nano particle is found to be 3 - 10 nm. The optical absorption characteristics are done by UV-Visible spectrophotometer. From the Tauc plots, the energy band gaps are calculated and because of their smaller size the particles have much higher band gap than the bulk material. The energy band gap is changed from 3.67 eV to 4.27 eV in citric acid coated copper quantum dots and 4.17 eV to 4.52 eV in CTAB coated copper quantum dots.

  16. Quinoxaline derivatives as corrosion inhibitors for mild steel in hydrochloric acid medium: Electrochemical and quantum chemical studies

    NASA Astrophysics Data System (ADS)

    Olasunkanmi, Lukman O.; Kabanda, Mwadham M.; Ebenso, Eno E.

    2016-02-01

    The corrosion inhibition potential of four quinoxaline derivatives namely, 1-[3-(4-methylphenyl)-5-(quinoxalin-6-yl)-4,5-dihydropyrazol-1-yl]butan-1-one (Me-4-PQPB), 1-(3-(4-methoxyphenyl)-5-(quinoxalin-6-yl)-4,5-dihydropyrazol-1-yl)butan-1-one (Mt-4-PQPB), 1-[3-(3-methoxyphenyl)-5-(quinoxalin-6-yl)-4,5-dihydropyrazol-1-yl]butan-1-one (Mt-3-PQPB) and 1-[3-(2H-1,3-benzodioxol-5-yl)-5-(quinoxalin-6-yl)-4,5-dihydropyrazol-1-yl]butan-1-one (Oxo-1,3-PQPB) was studied for mild steel corrosion in 1 M HCl solution using electrochemical, spectroscopic techniques and quantum chemical calculations. The results of both potentiodynamic polarization and electrochemical impedance spectroscopic studies revealed that the compounds are mixed-type inhibitors and the order of corrosion inhibition efficiency at 100 ppm is Me-4-PQPB>Mt-3-PQPB>Oxo-1,3-PQPB>Mt-4-PQPB. Fourier transform infrared (FTIR) and ultraviolet-visible (UV-vis) spectroscopic analyses confirmed the presence of chemical interactions between the inhibitors and mild steel surface. The adsorption of the inhibitor molecules on mild steel surface was found to be both physisorption and chemisorption but predominantly chemisorption. The experimental data obey Langmuir adsorption isotherm. Scanning electron microscopy studies revealed the formation of protective films of the inhibitors on mild steel surface. Quantum chemical parameters obtained from density functional theory (DFT) calculations support experimental results.

  17. Synthesis and characterization of CdSe quantum dots dispersed in PVA matrix by chemical route

    NASA Astrophysics Data System (ADS)

    Khan, Zubair M. S. H.; Ganaie, Mohsin; Khan, Shamshad A.; Husain, M.; Zulfequar, M.

    2016-05-01

    CdSe quantum dots using polyvinyl alcohol as a capping agent have been synthesized via a simple heat induced thermolysis technique. The structural analysis of CdSe/PVA thin film was studied by X-ray diffraction, which confirms crystalline nature of the prepared film. The surface morphology and particle size of the prepared sample was studied by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM). The SEM studies of CdSe/PVA thin film shows the average size of particles in the form of clusters of several quantum dots in the range of 10-20 nm. The morphology of CdSe/PVA thin film was further examined by TEM. The TEM image shows the fringes of tiny dots with average sizes of 4-7 nm. The optical properties of CdSe/PVA thin film were studied by UV-VIS absorption spectroscopy. The CdSe/PVA quantum dots follow the role of direct transition and the optical band gap is found to be 4.03 eV. From dc conductivity measurement, the observed value of activation energy was found to be 0.71 eV.

  18. Exciton scattering approach for branched conjugated molecules and complexes. II. Extraction of the exciton scattering parameters from quantum-chemical calculations.

    PubMed

    Wu, Chao; Malinin, Sergey V; Tretiak, Sergei; Chernyak, Vladimir Y

    2008-11-01

    We obtain the parameters of the exciton scattering (ES) model from the quantum-chemical calculations of the electronic excitations in simple phenylacetylene-based molecules. We determine the exciton dispersion and the frequency-dependent scattering matrices which describe scattering properties of the molecular ends as well as of meta- and orthoconjugated links. The extracted functions are smooth, which confirms the validity of the ES picture. We find a good agreement between the ES and quantum-chemical results for the excitation energies in simple test molecules. PMID:19045338

  19. Quantum chemical studies of some rhodanine azosulpha drugs as corrosion inhibitors for mild steel in acidic medium

    NASA Astrophysics Data System (ADS)

    Ebenso, Eno E.; Arslan, Taner; Kandemirli, Fatma; Caner, Necmettin; Love, Ian

    The density functional theory (DFT) at the B3LYP/6-31G (d,p) and B3LYP/6-311G(d,p) basis set levels and ab initio calculations using the HF/6-31G (d,p) and HF/6-311G(d,p) methods were performed on four rhodanine azosulpha drugs (namely 5-sulfadiazineazo-3-phenyl-2-thioxo-4-thiazolidinone, 5- sulfamethazineazo-3-phenyl-2-thioxo-4-thiazolidinone, 5-sulfadimethoxineazo-3-phenyl-2-thioxo- 4-thiazolidinone, and 5-sulfamethoxazoleazo-3-phenyl-2-thioxo-4-thiazolidinone) used as corrosion inhibitors for mild steel in acidic medium to determine the relationship between the molecular structure of the rhodanine azosulpha drugs and inhibition efficiency(%IE). The quantum chemical parameters/descriptors, namely, EHOMO (highest occupied molecular orbital energy), ELUMO (lowest unoccupied molecular orbital energy), the energy difference (ΔE) between EHOMO and ELUMO, dipole moment (μ), electron affinity (A), ionization potential (I), the absolute electronegativity (X), absolute hardness (η), softness (σ), polarizability (α), the Mulliken charges, and the fraction of electrons (ΔN) transfer from inhibitors to iron, were calculated and correlated with the experimental %IE. Quantitative structure activity relationship (QSAR) approach has been used, and a composite index of some quantum chemical parameters/descriptors was performed to characterize the inhibition performance of the studied molecules. The results showed that the inhibition efficiency (%IE) of the rhodanine azo sulfa drugs studied was closely related to some of the quantum chemical parameters/descriptors but with varying degrees of correlation coefficient (R2). The %IE also increased with the increase in EHOMO and decrease in EHOMO-ELUMO; and the areas containing N atoms are the most possible sites for bonding to the metal iron surface by donating electrons to the metal. The HOMO orbitals consist of 61.73-63.04% double bonded S atom (7(S)), and most of the rest are concentrated on the rhodanine group; so, the

  20. Quantum chemical calculations of interatomic potentials for computer simulation of solids

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A comprehensive mathematical model by which the collective behavior of a very large number of atoms within a metal or alloy can accurately be simulated was developed. Work was done in order to predict and modify the strength of materials to suit our technological needs. The method developed is useful in studying atomic interactions related to dislocation motion and crack extension.

  1. Accurate fast method with high chemical yield for determination of uranium isotopes (234U, 235U, 238U) in granitic samples using alpha spectroscopy

    NASA Astrophysics Data System (ADS)

    Guirguis, Laila A.; Farag, Nagdy M.; Salim, Adham K.

    2015-03-01

    The present study aims to use the α-spectroscopy at Nuclear Materials Authority (NMA) of Egypt. A radiochemical technique for analysis uranium isotopes was carried out for ten mineralized granitic samples together with the International standards RGU-1 (IAEA) and St4 (NMA). Several steps of sample preparation, radiochemical separation and source preparation were performed before analysis. Uranium was separated from sample matrix with 0.2 M TOPO in cyclohexane as an extracting agent with a chemical yield 98.95% then uranium was purified from lanthanides and actinides present with 0.2 M TOA in xylene as an extracting agent. The pure fraction was electrodeposited on a mirror-polished copper disc from buffer solution (NaHSO4+H2SO4+NH4OH). Rectangle pt-electrode with an anode-cathode distance of 2 cm was used. Current was 900 mA and the electrodeposition time reach up to 120 min. The achieved results show that the chemical yield ranged between 87.9±6.8 and 98±8.6.

  2. Standoff detection of explosives and chemical agents using broadly tuned external-cavity quantum cascade lasers (EC-QCLs)

    NASA Astrophysics Data System (ADS)

    Takeuchi, Eric B.; Rayner, Timothy; Weida, Miles; Crivello, Salvatore; Day, Timothy

    2007-10-01

    Civilian soft targets such as transportation systems are being targeted by terrorists using IEDs and suicide bombers. Having the capability to remotely detect explosives, precursors and other chemicals would enable these assets to be protected with minimal interruption of the flow of commerce. Mid-IR laser technology offers the potential to detect explosives and other chemicals in real-time and from a safe standoff distance. While many of these agents possess "fingerprint" signatures in the mid-IR (i.e. in the 3-20 micron regime), their effective interrogation by a practical, field-deployable system has been limited by size, complexity, reliability and cost constraints of the base laser technology. Daylight Solutions has addressed these shortcomings by developing compact, portable, broadly tunable mid-IR laser sources based upon external-cavity quantum cascade technology. This technology is now being applied by Daylight in system level architectures for standoff and remote detection of explosives, precursors and chemical agents. Several of these architectures and predicted levels of performance will be presented.

  3. A QUANTUM MECHANICAL STUDY OF STRUCTURAL AND ELECTRONIC DILUTION EFFECTS IN PARAMAGNETIC CHEMICAL EXCHANGE SATURATION TRANSFER AGENTS

    PubMed Central

    Miller, Whelton A.; Moore, Preston B.

    2014-01-01

    We present a computational study of the effect of chemical modifications of the meta and para substituents in the coordinating pendant arm of a modified 1,4,7,10-tetraazacyclododecane-N, N’, N″, N‴-tetraamide (DOTAM) ligand on the Chemical Exchange Saturation Transfer (CEST) signal. Magnetic Resonance Imaging (MRI) is currently one of the most widely used techniques available. MRI has led to a new class of pharmaceuticals termed “imagining” or “contrast” agents. These agents usually work by incorporating lanthanide metals such as Gadolinium (Gd) and Europium (Eu). This allows the contrast agents to take advantage of the paramagnetic properties of the metals, which in turn enhances the signal detectable by MRI. The effect of simple electron-withdrawing (e.g., nitro) and electron-donating (e.g., methyl) substituents chemically attached to a modified chelate arm (pendant arm) is quantified by charge transfer interactions in the coordinated water-chelate system computed from quantum mechanics. This study attempts to reveal the origin of the substituent effect on the CEST signal and the electronic structure of the complex. We find that the extent of Charge Transfer (CT) depends on orbital orientations and overlaps. However, CT interactions occur simultaneously from all arms, which causes a dilution effect with respect to the pendant arm. PMID:25485283

  4. A QUANTUM MECHANICAL STUDY OF STRUCTURAL AND ELECTRONIC DILUTION EFFECTS IN PARAMAGNETIC CHEMICAL EXCHANGE SATURATION TRANSFER AGENTS.

    PubMed

    Miller, Whelton A; Moore, Preston B

    2014-01-01

    We present a computational study of the effect of chemical modifications of the meta and para substituents in the coordinating pendant arm of a modified 1,4,7,10-tetraazacyclododecane-N, N', N″, N‴-tetraamide (DOTAM) ligand on the Chemical Exchange Saturation Transfer (CEST) signal. Magnetic Resonance Imaging (MRI) is currently one of the most widely used techniques available. MRI has led to a new class of pharmaceuticals termed "imagining" or "contrast" agents. These agents usually work by incorporating lanthanide metals such as Gadolinium (Gd) and Europium (Eu). This allows the contrast agents to take advantage of the paramagnetic properties of the metals, which in turn enhances the signal detectable by MRI. The effect of simple electron-withdrawing (e.g., nitro) and electron-donating (e.g., methyl) substituents chemically attached to a modified chelate arm (pendant arm) is quantified by charge transfer interactions in the coordinated water-chelate system computed from quantum mechanics. This study attempts to reveal the origin of the substituent effect on the CEST signal and the electronic structure of the complex. We find that the extent of Charge Transfer (CT) depends on orbital orientations and overlaps. However, CT interactions occur simultaneously from all arms, which causes a dilution effect with respect to the pendant arm. PMID:25485283

  5. Quantum-chemical studies on mutagenicity of aromatic and heteroaromatic amines.

    PubMed

    Borosky, Gabriela L

    2013-01-01

    Arylamines are well-known as widespread industrial and environmental mutagens and carcinogens. Their bioactivity stems from enzymatic metabolic activation to reactive and highly electrophilic intermediates. In this work, computational investigations related to the biological activity of these compounds have been reviewed, especially focusing on studies reporting results from quantum-mechanical calculations. Correlations between relative mutagenicities and structural and electronic features of the parent amines and of their derived nitrenium ion intermediates were examined, with the aim of achieving a clearer comprehension of the main factors determining the genotoxic potential of this type of compounds. PMID:23277072

  6. A comparative experimental and quantum chemical study on monomeric and dimeric structures of 3,5-dibromoanthranilic acid

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Cinar, Mehmet

    2012-10-01

    This study presents the structural and spectroscopic characterization of 3,5-dibromoanthranilic acid with help of experimental techniques (FT-IR, FT-Raman, UV, NMR) and quantum chemical calculations. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman in the range of 4000-400 and 4000-50 cm-1, respectively. The vibrational frequencies were also computed using B3LYP method of DFT with 6-311++G(d,p) basis set. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The 1H, 13C and DEPT NMR spectra were recorded in DMSO solution and calculated by gauge-invariant atomic orbitals (GIAO) method. The UV absorption spectra of the compound were recorded in the range of 200-400 nm in ethanol, water and DMSO solutions. Solvent effects were calculated using time-dependent density functional theory and CIS method. The ground state geometrical structure of compound was predicted by B3LYP method and compared with the crystallographic structure of similar compounds. All calculations were made for monomeric and dimeric structure of compound. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken atomic charges of neutral and anionic form of the molecule were computed and compared with anthranilic acid.

  7. Nonlinear absorption properties of AlGaAs/GaAs multiple quantum wells grown by metalorganic chemical vapor deposition

    NASA Technical Reports Server (NTRS)

    Lee, Hsing-Chung; Kost, A.; Kawase, M.; Hariz, A.; Dapkus, P. Daniel

    1988-01-01

    The nonlinear absorption properties of the excitonic resonances associated with multiple quantum wells (MQWs) in AlGaAs/GaAs grown by metalorganic chemical vapor deposition are reported. The dependence of the saturation properties on growth parameters, especially growth temperature, and the well width are described. The minimum measured saturation intensity for these materials is 250 W/sq cm, the lowest reported value to date. The low saturation intensities are the result of excellent minority carrier properties. A systematic study of minority carrier lifetimes in quantum wells are reported. Lifetimes range from 50-350 ns depending on growth temperature and well width. When corrected for lateral diffusion effects and the measured minority carrier lifetime, the saturation data suggest that saturation intensities as low as 2.3 W/sq cm can be achieved in this system. The first measurements of the dependence of the exciton area and the magnitude of the excitonic absorption on well width are prsented. The growth of MQW structures on transparent GaP substrates is demonstrated and the electroabsorption properties of these structures are reviewed.

  8. A comparative experimental and quantum chemical study on monomeric and dimeric structures of 3,5-dibromoanthranilic acid.

    PubMed

    Karabacak, Mehmet; Cinar, Mehmet

    2012-10-01

    This study presents the structural and spectroscopic characterization of 3,5-dibromoanthranilic acid with help of experimental techniques (FT-IR, FT-Raman, UV, NMR) and quantum chemical calculations. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman in the range of 4000-400 and 4000-50 cm(-1), respectively. The vibrational frequencies were also computed using B3LYP method of DFT with 6-311++G(d,p) basis set. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The (1)H, (13)C and DEPT NMR spectra were recorded in DMSO solution and calculated by gauge-invariant atomic orbitals (GIAO) method. The UV absorption spectra of the compound were recorded in the range of 200-400 nm in ethanol, water and DMSO solutions. Solvent effects were calculated using time-dependent density functional theory and CIS method. The ground state geometrical structure of compound was predicted by B3LYP method and compared with the crystallographic structure of similar compounds. All calculations were made for monomeric and dimeric structure of compound. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken atomic charges of neutral and anionic form of the molecule were computed and compared with anthranilic acid. PMID:22871548

  9. Electronic states of benzo[a]pyrene. Linear and magnetic circular dichroism, polarized fluorescence, and quantum chemical calculations

    SciTech Connect

    Spanget-Larsen, J.; Waluk, J.; Erikksson, S.

    1992-03-11

    The carcinogen benzo[a]pyrene is investigated by UV and IR linear dichroism (LD) spectroscopy in stretched polyethylene, by UV magnetic circular dichroism (MCD) spectroscopy, and by fluorescence polarization spectroscopy. The combined results lead to detailed experimental characterization of transitions in the near-UV region, with determination of polarization directions for five electronic transitions. The experimental results are compared with theoretical predictions using the PPP, CNDO/S, CNDO-SDCI, and LCOAO quantum chemical models. Excellent agreement with observed values in the low-energy region, including transition transition moment directions and MCD signs, is obtained within the LCOAO model. The theoretical analysis reveals a strong breakdown of the alternant pairing symmetry for benzo[a]pyrene, compared with those observed in the related hydrocarbons benz[a]anthracene and chrysene. 44 refs., 7 figs., 4 tabs.

  10. Formation and dissociation of protonated cytosine—cytosine base pairs in i-motifs by ab initio quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Hu; Li, Ming; Wang, Yan-Ting; Ouyang, Zhong-Can

    2014-02-01

    Formation and dissociation mechanisms of C—C+ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C—C+ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C—C+ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

  11. A modular architecture for multi-channel external cavity quantum cascade laser-based chemical sensors: a systems approach

    SciTech Connect

    Taubman, Matthew S.; Myers, Tanya L.; Bernacki, Bruce E.; Stahl, Robert D.; Cannon, Bret D.; Schiffern, John T.; Phillips, Mark C.

    2012-04-01

    A multi-channel laser-based chemical sensor platform is presented, in which a modular architecture allows the exchange of complete sensor channels without disruption to overall operation. Each sensor channel contains custom optical and electronics packages, which can be selected to access laser wavelengths, interaction path lengths and modulation techniques optimal for a given application or mission. Although intended primarily to accommodate mid-infrared (MIR) external cavity quantum cascade lasers (ECQCLs)and astigmatic Herriott cells, channels using visible or near infrared (NIR) lasers or other gas cell architectures can also be used, making this a truly versatile platform. Analog and digital resources have been carefully chosen to facilitate small footprint, rapid spectral scanning, ow-noise signal recovery, failsafe autonomous operation, and in-situ chemometric data analysis, storage and transmission. Results from the demonstration of a two-channel version of this platform are also presented.

  12. Mechanism of the Fischer indole synthesis. Quantum-chemical interpretation of the rearrangement of substituted cyclohexanone arylhydrazones to tetrahydrocarbazoles

    SciTech Connect

    Vysotskii, Yu.B.; Przheval'skii, N.M.; Zemskii, B.P.; Grandberg, I.I.; Kostromina, L.Yu.

    1987-01-01

    Calculations of a number of model structures within the scheme of the Fischer indole synthesis were made on the basis of a bonding variant of perturbation theory in the self-consistent-field (SCF) MO LCAO method. A quantum-chemical interpretation of the effect of substituents on the course of the thermal process is given. The kinetics of the thermal and acid-catalyzed indolization of substituted cyclohexanone arylhydrazones to tetrahydrocarbazoles were studied by spectrophotometry. It was shown that the experimental data are in satisfactory agreement with the calculated values. It was concluded that a concerted mechanism (a (3,3)-sigma-tropic shift) for the step involving the formation of a carbon-carbon bond in the Fischer reaction is preferred.

  13. Atmospheric-pressure epitaxial growth technique of a multiple quantum well by mist chemical vapor deposition based on Leidenfrost droplets

    NASA Astrophysics Data System (ADS)

    Kawaharamura, Toshiyuki; Dang, Giang T.; Nitta, Noriko

    2016-10-01

    A multiple quantum well α-Fe2O3/α-Ga2O3 with parallel and coherent formation of uniform and highly single-crystalline layers on a sapphire substrate has been fabricated by open-air atmospheric-pressure solution-processed mist chemical vapor deposition (Mist CVD). This report demonstrates that complicated structures with atomic-level control can be fabricated even in non-vacuum conditions by the Mist CVD. This can be achieved via the precise control of the precursor flow and ambient temperature combined with the formation of mist droplets of the special Leidenfrost state, which increased the atomic migration length by 108 times more than that of traditional vacuum techniques. This work could be a milestone in the transformation from vacuum to non-vacuum thin film deposition techniques towards a green and sustainable industry.

  14. Quantum chemical MP2 results on some hydrates of cytosine: binding sites, energies and the first hydration shell.

    PubMed

    Fogarasi, Géza; Szalay, Péter G

    2015-11-28

    A detailed quantum chemical investigation was undertaken to obtain the structure and energetics of cytosine hydrates Cyt·nH2O, with n = 1 to 7. The MP2(fc)/aug-cc-pVDZ level was used as the standard, with some DFT (B3LYP) and coupled cluster calculations, as well as calculations with the aug-cc-pVTZ basis set added for comparison. In a systematic search for microhydrated forms of cytosine, we have found that several structures have not yet been reported in the literature. The energies of different isomers, as well as binding energies are compared. When predicting the stability of a complex, we suggest using a scheme where the water molecules are extracted from a finite model of bulk water. Finally, based on energetic data, we suggest a rational definition of the first hydration shell; with this definition, it contains just six water molecules. PMID:26487481

  15. [Intramolecular hygrogen bonds in conformers of 2'-deoxycytidine: results of quantum-chemical analysis of electron density topology].

    PubMed

    Zhurakivs'kyĭ, R O; Hovorun, D M

    2006-01-01

    As many as 13 types of intramolecular hygrogen bonds are determined in 89 conformers of 2'-deoxycytidine nucleoside by means of quantum-chemical analysis (at DFT B3LYP/6-31G(d,p) theory level) of electron density topology with Atoms-in-Molecules (AIM) theory. The total number of H-bonds is 168 and their types are C1'H...O2, C2'H2...O5', C2'H2...O2, C3'H...O2, C5'H1...O2, C5'H2...O2, C6H...O4', C6H...O5', C3'H...HC6, O3'H...O5', O5'H...O3', O5'H...O4' and O5'H...O2. Conformational, geometric and electron-topological properties of H-bonds are presented.

  16. Accurate quantum chemical modelling of the separation of Eu(3+) from Am(3+)/Cm(3+) by liquid-liquid extraction with Cyanex272.

    PubMed

    Cao, Xiaoyan; Zhang, Jun; Weissmann, Daniel; Dolg, Michael; Chen, Xuebo

    2015-08-28

    The experimentally observed extraction complexes of trivalent lanthanide Eu(3+) and actinide Am(3+)/Cm(3+) cations with Cyanex272 [bis(2,4,4-trimethylpentyl) phosphinic acid, denoted as HC272] and Cyanex301 [bis(2,4,4-trimethylpentyl) dithiophosphinic acid, denoted as HC301] have been studied by using relativistic energy-consistent 4f- and 5f-in-core pseudopotentials for trivalent f elements, combined with density functional theory and a continuum solvation model. It has been found that, as a result of hydrogen bonding, HC272 exists primarily as a self-associated species, whereas HC301 is preferably a monomer. The calculations show that in case of all three M(3+) (M = Eu, Am, Cm) ions for HC272 the extraction complexes M[H(C272)2]3 are formed prior to M(C272)3, whereas for HC301 the extraction complexes M(C301)3 have priority over M[H(C301)2]3. The calculated M-O and M-S bond lengths and the M-P distances of these preferred extraction complexes agree very well with the available experimental data. The obtained changes of the Gibbs free energies in the liquid-liquid extraction reactions (1): Maqu(3+) + 3(HC272)2,org→ M[H(C272)2]3,org + 3Haqu(+) and (2): Maqu(3+) + 3HC301org→ M(C301)3,org + 3Haqu(+) agree with the experimentally observed thermodynamical priorities of HC272 and HC301, i.e., HC272 prefers Eu(3+) over Am(3+)/Cm(3+) and HC301 prefers Am(3+)/Cm(3+) over Eu(3+). The obtained changes of the Gibbs free energies in reaction (2) (Eu, 68.1 kJ mol(-1); Am, 46.5 kJ mol(-1)) agree quite well with the experimental findings (Eu, 63.3 kJ mol(-1); Am, 44.1 kJ mol(-1)). PMID:26203895

  17. Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors

    PubMed Central

    2013-01-01

    Background In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Results Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. Conclusions A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation. PMID:24171724

  18. Remote explosive and chemical agent detection using broadly tunable mid-infrared external cavity quantum cascade lasers

    NASA Astrophysics Data System (ADS)

    Rayner, Timothy; Weida, Miles; Pushkarsky, Michael; Day, Timothy

    2007-04-01

    Terrorists both with IEDs and suicide bombers are targeting civilian infrastructures such as transportation systems. Although explosive detection technologies exist and are used effectively in aviation, these technologies do not lend themselves well to protecting open architecture soft targets, as they are focused on a checkpoint form factor that limits throughput. However, remote detection of explosives and other chemicals would enable these kinds of targets to be protected without interrupting the flow of commerce. Tunable mid-IR laser technology offers the opportunity to detect explosives and other chemicals remotely and quickly. Most chemical compounds, including explosives, have their fundamental vibrational modes in the mid-infrared region (3 to 15μm). There are a variety of techniques that focus on examining interactions that have proven effective in the laboratory but could never work in the field due to complexity, size, reliability and cost. Daylight Solutions has solved these problems by integrating quantum cascade gain media into external tunable cavities. This has resulted in miniaturized, broadly tunable mid-IR laser sources. The laser sources have a capability to tune to +/- 5% of their center wavelength, which means they can sweep through an entire absorption spectrum to ensure very good detection and false alarm performance compared with fixed wavelength devices. These devices are also highly portable, operate at room temperature, and generate 10's to 100's of mW in optical power, in pulsed and continuous wave configurations. Daylight Solutions is in the process of developing a variety of standoff explosive and chemical weapon detection systems using this technology.

  19. Conceptual versus Algorithmic Learning in High School Chemistry: The Case of Basic Quantum Chemical Concepts--Part 2. Students' Common Errors, Misconceptions and Difficulties in Understanding

    ERIC Educational Resources Information Center

    Papaphotis, Georgios; Tsaparlis, Georgios

    2008-01-01

    Part 2 of the findings are presented of a quantitative study (n = 125) on basic quantum chemical concepts taught at twelfth grade (age 17-18 years) in Greece. A paper-and-pencil test of fourteen questions was used that were of two kinds: five questions that tested recall of knowledge or application of algorithmic procedures (type-A questions);…

  20. Determination of enthalpies of formation of energetic molecules with composite quantum chemical methods

    NASA Astrophysics Data System (ADS)

    Manaa, M. Riad; Fried, Laurence E.; Kuo, I.-Feng W.

    2016-03-01

    We report gas-phase enthalpies of formation for the set of energetic molecules NTO, DADE, LLM-105, TNT, RDX, TATB, HMX, and PETN using the G2, G3, G4, and ccCA-PS3 quantum composite methods. Calculations for HMX and PETN hitherto represent the largest molecules attempted with these methods. G3 and G4 calculations are typically close to one another, with a larger difference found between these methods and ccCA-PS3. Although there is significant uncertainty in experimental values, the mean absolute deviation between the average experimental value and calculations are 12, 6, 7, and 3 kcal/mol for G2, G3, G4, and ccCA-PS3, respectively.

  1. Potential Energy Surfaces for Reaction Catalyzed by Metalloenzymes from Quantum Chemical Computations

    NASA Astrophysics Data System (ADS)

    Leopoldini, Monica; Marino, Tiziana; Russo, Nino; Toscano, Marirosa

    For several decades quantum mechanical (QM) computational methods have been developed and refined so that it was possible to extend their applicability field enormously. Today, they are used generally to supplement experimental techniques because the theory also affords deeper understanding of molecular processes that cannot be obtained from experiments alone. Due to their favorable scaling when compared to the ab initiomethods, density functional theory (DFT) approach allows the treatment of very large systems such as the biomolecules. Thus, now it is possible, for instance, to study the difficult and critical reactions catalyzed by enzymes in biological systems. Here, a brief account of the studies performed on different metalloenzymes is given, focusing on methods and models used to describe their reaction mechanisms.

  2. Model of the catalytic mechanism of human aldose reductase based on quantum chemical calculations.

    SciTech Connect

    Cachau, R. C.; Howard, E. H.; Barth, P. B.; Mitschler, A. M.; Chevrier, B. C.; Lamour, V.; Joachimiak, A.; Sanishvili, R.; Van Zandt, M.; Sibley, E.; Moras, D.; Podjarny, A.; UPR de Biologie Structurale; National Cancer Inst.; Univ. Louis Pasteur; Inst. for Diabetes Discovery, Inc.

    2000-01-01

    Aldose Reductase is an enzyme involved in diabetic complications, thoroughly studied for the purpose of inhibitor development. The structure of an enzyme-inhibitor complex solved at sub-atomic resolution has been used to develop a model for the catalytic mechanism. This model has been refined using a combination of Molecular Dynamics and Quantum calculations. It shows that the proton donation, the subject of previous controversies, is the combined effect of three residues: Lys 77, Tyr 48 and His 110. Lys 77 polarises the Tyr 48 OH group, which donates the proton to His 110, which becomes doubly protonated. His 110 then moves and donates the proton to the substrate. The key information from the sub-atomic resolution structure is the orientation of the ring and the single protonafion of the His 110 in the enzyme-inhibitor complex. This model is in full agreement with all available experimental data.

  3. Quantum cascade laser based active hyperspectral imaging for standoff detection of chemicals on surfaces

    NASA Astrophysics Data System (ADS)

    Hugger, S.; Fuchs, F.; Jarvis, J.; Yang, Q. K.; Rattunde, M.; Ostendorf, R.; Schilling, C.; Driad, R.; Bronner, W.; Aidam, R.; Wagner, J.; Tybussek, T.; Rieblinger, K.

    2016-02-01

    We employ active hyperspectral imaging using tunable mid-infrared (MIR) quantum cascade lasers for contactless identification of solid and liquid contaminations on surfaces. By collecting the backscattered laser radiation with a camera, a hyperspectral data cube, containing the spatially resolved spectral information of the scene is obtained. Data is analyzed using appropriate algorithms to find the target substances even on substrates with a priori unknown spectra. Eye-save standoff detection of residues of explosives and precursors over extended distances is demonstrated and the main purpose of our system. However, it can be applied to any substance with characteristic reflectance / absorbance spectrum. As an example, we present first results of monitoring food quality by distinguishing fresh and mold contaminated peanuts by their MIR backscattering spectrum.

  4. Determination of enthalpies of formation of energetic molecules with composite quantum chemical methods

    DOE PAGES

    Manaa, M. Riad; Fried, Laurence E.; Kuo, I-Feng W.

    2016-02-01

    We report gas-phase enthalpies of formation for the set of energetic molecules NTO, DADE, LLM-105, TNT, RDX, TATB, HMX, and PETN using the G2, G3, G4, and ccCA-PS3 quantum composite methods. Calculations for HMX and PETN hitherto represent the largest molecules attempted with these methods. G3 and G4 calculations are typically close to one another, with a larger difference found between these methods and ccCA-PS3. Furthermore there is significant uncertainty in experimental values, the mean absolute deviation between the average experimental value and calculations are 12, 6, 7, and 3 kcal/mol for G2, G3, G4, and ccCA-PS3, respectively.

  5. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

    The application of ab initio quantum mechanical approaches in the study of metal atom clusters requires simplifying techniques that do not compromise the reliability of the calculations. Various aspects of the implementation of the effective core potential (ECP) technique for the removal of the metal atom core electrons from the calculation were examined. The ECP molecular integral formulae were modified to bring out the shell characteristics as a first step towards fulfilling the increasing need to speed up the computation of the ECP integrals. Work on the relationships among the derivatives of the molecular integrals that extends some of the techniques pioneered by Komornicki for the calculation of the gradients of the electronic energy was completed and a formulation of the ECP approach that quite naturally unifies the various state-of-the-art "shape- and Hamiltonian-consistent" techniques was discovered.

  6. Rotational Spectrum, Conformational Composition, and Quantum Chemical Calculations of Cyanomethyl Formate (HC(O)OCH2C≡N), a Compound of Potential Astrochemical Interest.

    PubMed

    Samdal, Svein; Møllendal, Harald; Carles, Sophie

    2015-08-27

    The rotational spectrum of cyanomethyl formate (HC(O)OCH2C≡N) has been recorded in the 12–123 GHz spectral range. The spectra of two conformers were assigned. The rotamer denoted I has a symmetry plane and two out-of plane hydrogen atoms belonging to the cyanomethyl (CH2CN) moiety. In the conformer called II, the cyanomethyl group is rotated 80.3° out of this plane. Conformer I has an energy that is 1.4(6) kJ/mol lower than the energy of II according to relative intensity measurements. A large number of rotational transitions have been assigned for the ground and vibrationally excited states of the two conformers and accurate spectroscopic constants have been obtained. These constants should predict frequencies of transitions outside the investigated spectral range with a very high degree of precision. It is suggested that cyanomethyl formate is a potential interstellar compound. This suggestion is based on the fact that its congener methyl formate (HC(O)OCH3) exists across a large variety of interstellar environments and the fact that cyanides are very prevalent in the Universe. The experimental work has been augmented by high-level quantum chemical calculations. The CCSD/cc-pVQZ calculations are found to predict structures of the two forms that are very close to the Born–Oppenheimer equilibrium structures. MP2/cc-pVTZ predictions of several vibration–rotation interaction constants were generally found to be rather inaccurate. A gas-phase reaction between methyl formate and the cyanomethyl radical CH2CN to produce a hydrogen atom and cyanomethyl formate was mimicked using MP2/cc-pVTZ calculations. It was found that this reaction is not favored thermodynamically. It is also conjectured that the possible formation of cyanomethyl formate might be catalyzed and take place on interstellar particles. PMID:26207519

  7. Potential interstellar noble gas molecules: ArOH+ and NeOH+ rovibrational analysis from quantum chemical quartic force fields

    NASA Astrophysics Data System (ADS)

    Theis, Riley A.; Fortenberry, Ryan C.

    2016-03-01

    The discovery of ArH+ in the interstellar medium has shown that noble gas chemistry may be of more chemical significance than previously believed. The present work extends the known chemistry of small noble gas molecules to NeOH+ and ArOH+. Besides their respective neonium and argonium diatomic cation cousins, these hydroxyl cation molecules are the most stable small noble gas molecules analyzed of late. ArOH+ is once again more stable than the neon cation, but both are well-behaved enough for a complete quartic force field analysis of their rovibrational properties. The Ar-O bond in ArOH+ , for instance, is roughly three-quarters of the strength of the Ar-H bond in ArH+ highlighting the rigidity of this system. The rotational constants, geometries, and vibrational frequencies for both molecules and their various isotopologues are computed from ab initio quantum chemical theory at high-level, and it is shown that these cations may form in regions where peroxy or weakly-bound alcohols may be present. The resulting data should be of significant assistance for the laboratory or observational analysis of these potential interstellar molecules.

  8. Design and performance of a sensor system for detection of multiple chemicals using an external cavity quantum cascade laser

    NASA Astrophysics Data System (ADS)

    Phillips, Mark C.; Taubman, Matthew S.; Bernacki, Bruce E.; Cannon, Bret D.; Schiffern, John T.; Myers, Tanya L.

    2010-01-01

    We describe the performance of a sensor system designed for simultaneous detection of multiple chemicals with both broad and narrow absorption features. The sensor system consists of a broadly tunable external cavity quantum cascade laser (ECQCL), multi-pass Herriott cell, and custom low-noise electronics. The ECQCL features a fast wavelength tuning rate of 2265 cm-1/s (15660 nm/s) over the range of 1150-1270 cm-1 (7.87-8.70 μm), which permits detection of molecules with broad absorption features and dynamic concentrations, while the 0.2 cm-1 spectral resolution of the ECQCL system allows measurement of small molecules with atmospherically broadened absorption lines. High-speed amplitude modulation and low-noise electronics are used to improve the ECQCL performance for direct absorption measurements. We demonstrate simultaneous detection of Freon-134a (1,1,1,2-tetrafluoroethane), ammonia (NH3), and nitrous oxide (N2O) at low-ppb concentrations in field measurements of atmospheric chemical releases from a point source.

  9. Design and Performance of a Sensor System for Detection of Multiple Chemicals Using an External Cavity Quantum Cascade Laser

    SciTech Connect

    Phillips, Mark C.; Taubman, Matthew S.; Bernacki, Bruce E.; Cannon, Bret D.; Schiffern, John T.; Myers, Tanya L.

    2010-01-23

    We describe the performance of a sensor system designed for simultaneous detection of multiple chemicals with both broad and narrow absorption features. The sensor system consists of a broadly tunable external cavity quantum cascade laser (ECQCL), multi-pass Herriott cell, and custom low-noise electronics. The ECQCL features a rapid wavelength tuning rate of 2265 cm 1/s (15660 nm/s) over its tuning range of 1150-1270 cm 1 (7.87-8.70 μm), which permits detection of molecules with broad absorption features and dynamic concentrations, while the 0.2 cm-1 spectral resolution of the ECQCL system allows measurement of small molecules with atmospherically broadened absorption lines. High-speed amplitude modulation and low-noise electronics are used to improve the ECQCL performance for direct absorption measurements. We demonstrate simultaneous detection of Freon-134a (1,1,1,2-tetrafluoroethane), ammonia (NH3), and nitrous oxide (N2O) at low-ppb concentrations in field measurements of atmospheric chemical releases from a point source.

  10. New insights into the tropospheric oxidation of isoprene: combining field measurements, laboratory studies, chemical modelling and quantum theory.

    PubMed

    Whalley, Lisa; Stone, Daniel; Heard, Dwayne

    2014-01-01

    In this chapter we discuss some of the recent work directed at further understanding the chemistry of our atmosphere in regions of low NO x , such as forests, where there are considerable emissions of biogenic volatile organic compounds, for example reactive hydrocarbons such as isoprene. Recent field measurements have revealed some surprising results, for example that OH concentrations are measured to be considerably higher than can be understood using current chemical mechanisms. It has also not proven possible to reconcile field measurements of other species, such as oxygenated VOCs, or emission fluxes of isoprene, using current mechanisms. Several complementary approaches have been brought to bear on formulating a solution to this problem, namely field studies using state-of-the-art instrumentation, chamber studies to isolate sub-sections of the chemistry, laboratory studies to measure rate coefficients, product branching ratios and photochemical yields, the development of ever more detailed chemical mechanisms, and high quality ab initio quantum theory to calculate the energy landscape for relevant reactions and to enable the rates of formation of products and intermediates for previously unknown and unstudied reactions to be predicted. The last few years have seen significant activity in this area, with several contrasting postulates put forward to explain the experimental findings, and here we attempt to synthesise the evidence and ideas.

  11. Comparative electron paramagnetic resonance investigation of reduced graphene oxide and carbon nanotubes with different chemical functionalities for quantum dot attachment

    SciTech Connect

    Pham, Chuyen V.; Krueger, Michael E-mail: emre.erdem@physchem.uni-freiburg.de; Eck, Michael; Weber, Stefan; Erdem, Emre E-mail: emre.erdem@physchem.uni-freiburg.de

    2014-03-31

    Electron paramagnetic resonance (EPR) spectroscopy has been applied to different chemically treated reduced graphene oxide (rGO) and multiwalled carbon nanotubes (CNTs). A narrow EPR signal is visible at g = 2.0029 in both GO and CNT-Oxide from carbon-related dangling bonds. EPR signals became broader and of lower intensity after oxygen-containing functionalities were reduced and partially transformed into thiol groups to obtain thiol-functionalized reduced GO (TrGO) and thiol-functionalized CNT (CNT-SH), respectively. Additionally, EPR investigation of CdSe quantum dot-TrGO hybrid material reveals complete quenching of the TrGO EPR signal due to direct chemical attachment and electronic coupling. Our work confirms that EPR is a suitable tool to detect spin density changes in different functionalized nanocarbon materials and can contribute to improved understanding of electronic coupling effects in nanocarbon-nanoparticle hybrid nano-composites promising for various electronic and optoelectronic applications.

  12. B36 borophene as an electronic sensor for formaldehyde: Quantum chemical analysis

    NASA Astrophysics Data System (ADS)

    Shahbazi Kootenaei, Amirhossein; Ansari, Goodarz

    2016-08-01

    Pristine carbon nanotubes and graphene show great sensitivity toward several lethal gases but cannot identify some extremely toxic chemicals such as formaldehyde (HCOH). Recent successful synthesis of all-boron graphene-like sheets attracted strong interest in exploring their possible applications. Herein, we inspected the potential application of B36 borophene sheet as a sensor for HCOH detection, using density functional theory computations. Different theoretical levels including B97D and Minnesota 06 functionals with different basis sets were employed. It was predicted that the electrical conductivity of B36 borophene significantly increases at the presence of HCOH molecules, thereby generating an electrical signal. The electrical signal is increased by increasing the number of adsorbed HCOH molecules, indicating that this sensor is sensitive to the concentration (or pressure) of HCOH gas. These results suggest that the pristine borophene may be used in the HCOH chemical sensors.

  13. Quantum origins of the Iczkowski-Margrave model of chemical potential

    SciTech Connect

    Valone, Steven M

    2010-01-01

    Charge flow in materials is controlled at the atomistic level through some model of the chemical potential, such as the Iczkowski-Margrave (IM) model. This model is built largely on heuristic arguments. Here a model Hamiltonian is constructed at the atomistic level commensurate with the IM model. Essential properties of the model Hamiltonian are presented, including a possible revision of the charge dependence in the IM model. Transitional properties of the model are shown to be central to regulating charge flow.

  14. The role of NH3 and hydrocarbon mixtures in GaN pseudo-halide CVD: a quantum chemical study.

    PubMed

    Gadzhiev, Oleg B; Sennikov, Peter G; Petrov, Alexander I; Kachel, Krzysztof; Golka, Sebastian; Gogova, Daniela; Siche, Dietmar

    2014-11-01

    The prospects of a control for a novel gallium nitride pseudo-halide vapor phase epitaxy (PHVPE) with HCN were thoroughly analyzed for hydrocarbons-NH3-Ga gas phase on the basis of quantum chemical investigation with DFT (B3LYP, B3LYP with D3 empirical correction on dispersion interaction) and ab-initio (CASSCF, coupled clusters, and multireference configuration interaction including MRCI+Q) methods. The computational screening of reactions for different hydrocarbons (CH4, C2H6, C3H8, C2H4, and C2H2) as readily available carbon precursors for HCN formation, potential chemical transport agents, and for controlled carbon doping of deposited GaN was carried out with the B3LYP method in conjunction with basis sets up to aug-cc-pVTZ. The gas phase intermediates for the reactions in the Ga-hydrocarbon systems were predicted at different theory levels. The located π-complexes Ga…C2H2 and Ga…C2H4 were studied to determine a probable catalytic activity in reactions with NH3. A limited influence of the carbon-containing atmosphere was exhibited for the carbon doping of GaN crystal in the conventional GaN chemical vapor deposition (CVD) process with hydrocarbons injected in the gas phase. Our results provide a basis for experimental studies of GaN crystal growth with C2H4 and C2H2 as auxiliary carbon reagents for the Ga-NH3 and Ga-C-NH3 CVD systems and prerequisites for reactor design to enhance and control the PHVPE process through the HCN synthesis.

  15. Computational tests of quantum chemical models for structures, vibrational frequencies, and heats of formation of molecules with phosphorus and sulfur atoms.

    PubMed

    Hahn, David K; RaghuVeer, Krishans S; Ortiz, J V

    2010-08-12

    The Gaussian-n, complete basis set, and Weizmann-1 quantum chemical models for heats of formation are applied to a set of molecules with relevance to the combustion or pyrolysis of chemical warfare materials. Most of these models generate standard deviations from experiment that are less than 2 kcal/mol. The structures and vibrational frequencies that are generated in the course of these calculations are in good agreement with experimental data. Detailed comparisons with respect to structural types indicate that the present computational models are likely to generate useful data for complex models of combustion and pyrolysis of chemical warfare materials.

  16. Combined Quantum Chemical/Raman Spectroscopic Analyses of Li+ Cation Solvation: Cyclic Carbonate Solvents - Ethylene Carbonate and Propylene Earbonate

    SciTech Connect

    Allen, Joshua L.; Borodin, Oleg; Seo, D. M.; Henderson, Wesley A.

    2014-12-01

    Combined computational/Raman spectroscopic analyses of ethylene carbonate (EC) and propylene carbonate (PC) solvation interactions with lithium salts are reported. It is proposed that previously reported Raman analyses of (EC)n-LiX mixtures have utilized faulty assumptions. In the present studies, density functional theory (DFT) calculations have provided corrections in terms of both the scaling factors for the solvent's Raman band intensity variations and information about band overlap. By accounting for these factors, the solvation numbers obtained from two different EC solvent bands are in excellent agreement with one another. The same analysis for PC, however, was found to be quite challenging. Commercially available PC is a racemic mixture of (S)- and (R)-PC isomers. Based upon the quantum chemistry calculations, each of these solvent isomers may exist as multiple conformers due to a low energy barrier for ring inversion, making deconvolution of the Raman bands daunting and inherently prone to significant error. Thus, Raman spectroscopy is able to accurately determine the extent of the EC...Li+ cation solvation interactions using the provided methodology, but a similar analysis of PC...Li+ cation solvation results in a significant underestimation of the actual solvation numbers.

  17. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

    PubMed

    Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K; Chibotaru, Liviu F; Delcey, Mickaël G; De Vico, Luca; Fdez Galván, Ignacio; Ferré, Nicolas; Frutos, Luis Manuel; Gagliardi, Laura; Garavelli, Marco; Giussani, Angelo; Hoyer, Chad E; Li Manni, Giovanni; Lischka, Hans; Ma, Dongxia; Malmqvist, Per Åke; Müller, Thomas; Nenov, Artur; Olivucci, Massimo; Pedersen, Thomas Bondo; Peng, Daoling; Plasser, Felix; Pritchard, Ben; Reiher, Markus; Rivalta, Ivan; Schapiro, Igor; Segarra-Martí, Javier; Stenrup, Michael; Truhlar, Donald G; Ungur, Liviu; Valentini, Alessio; Vancoillie, Steven; Veryazov, Valera; Vysotskiy, Victor P; Weingart, Oliver; Zapata, Felipe; Lindh, Roland

    2016-02-15

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. PMID:26561362

  18. Quantum chemical study on surface complex structures of phosphate on gibbsite

    NASA Astrophysics Data System (ADS)

    Luengo, Carina V.; Castellani, Norberto J.; Ferullo, Ricardo M.

    2015-08-01

    Quantum mechanics calculations based on the density functional theory (DFT) were used to identify phosphate surface complexes on gibbsite at low and high pH. The different phosphate species were represented using the Al6(OH)18(H2O)6 cluster model considering four different geometries: monodentate mononuclear (Pmm), monodentate binuclear (Pmb), bidentate mononuclear (Pbm) and bidentate binuclear (Pbb). The corresponding adsorption reactions were modelled via ligand exchange between phosphate species and surface functional groups (hydroxyls and protonated hydroxyls at high and low pH, respectively). The theoretical results indicate that phosphate surface complexes are thermodynamically more favored at acid pH, in agreement with experimental evidences. The first step in these reactions, i.e., the generation of required aluminum vacant sites, was predicted to be particularly favorable when singly coordinated aquo groups are released. Stretching and bending vibrational frequencies associated with the different surface structures were calculated at both pH conditions. The corresponding values at low pH were found to be shifted to higher frequencies with respect to those ones at high pH. ATR-FTIR studies were also carried out. The resulting spectra are dominated by a strong band within the 800-840 cm-1 interval due to P-OH stretching modes. The corresponding peak appearing around 820 cm-1 at high pH is shifted to lower frequencies with respect to the position at low pH, a tendency well predicted by DFT calculations.

  19. ORBKIT: A modular python toolbox for cross-platform postprocessing of quantum chemical wavefunction data.

    PubMed

    Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe; Paulus, Beate; Hege, Hans-Christian; Schild, Axel

    2016-06-15

    ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. © 2016 Wiley Periodicals, Inc. PMID:27043934

  20. Synthesis, characterization, antibacterial activity and quantum chemical studies of N'-Acetyl propane sulfonic acid hydrazide

    NASA Astrophysics Data System (ADS)

    Alyar, Saliha; Alyar, Hamit; Ozdemir, Ummuhan Ozmen; Sahin, Omer; Kaya, Kerem; Ozbek, Neslihan; Gunduzalp, Ayla Balaban

    2015-08-01

    A new N'-Acetyl propane sulfonic acid hydrazide, C3H7sbnd SO2sbnd NHsbnd NHsbnd COCH3 (Apsh, an sulfon amide compound) has been synthesized for the first time. The structure of Apsh was investigated using elemental analysis, spectral (IR, 1H/13C NMR) measurements. In addition, molecular structure of the Apsh was determined by single crystal X-ray diffraction technique and found that the compound crystallizes in monoclinic, space group P 21/c. 1H and 13C shielding tensors for crystal structure were calculated with GIAO/DFT/B3LYP/6-311++G(d,p) methods in CDCl3. The structure of Apsh is optimized using Density Functional Theory (DFT) method. The vibrational band assignments were performed at B3LYP/6-311++G(d,p) theory level combined with scaled quantum mechanics force field (SQMFF) methodology. The theoretical IR frequencies are found to be in good agreement with the experimental IR frequencies. Nonlinear optical (NLO) behaviour of Apsh is also examined by the theoretically predicted values of dipole moment (μ), polarizability (α0) and first hyperpolarizability (βtot). The antibacterial activities of synthesized compound were studied against Gram positive bacteria: Staphylococcus aureus ATCC 25923, Enterococcus faecalis ATCC 23212, Staphylococcus epidermidis ATCC 34384, Gram negative bacteria: Eschericha coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae ATCC 70063 by using microdilution method (as MICs) and disc diffusion method.

  1. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

    PubMed

    Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K; Chibotaru, Liviu F; Delcey, Mickaël G; De Vico, Luca; Fdez Galván, Ignacio; Ferré, Nicolas; Frutos, Luis Manuel; Gagliardi, Laura; Garavelli, Marco; Giussani, Angelo; Hoyer, Chad E; Li Manni, Giovanni; Lischka, Hans; Ma, Dongxia; Malmqvist, Per Åke; Müller, Thomas; Nenov, Artur; Olivucci, Massimo; Pedersen, Thomas Bondo; Peng, Daoling; Plasser, Felix; Pritchard, Ben; Reiher, Markus; Rivalta, Ivan; Schapiro, Igor; Segarra-Martí, Javier; Stenrup, Michael; Truhlar, Donald G; Ungur, Liviu; Valentini, Alessio; Vancoillie, Steven; Veryazov, Valera; Vysotskiy, Victor P; Weingart, Oliver; Zapata, Felipe; Lindh, Roland

    2016-02-15

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

  2. Cluster analysis of the DrugBank chemical space using molecular quantum numbers.

    PubMed

    Awale, Mahendra; Reymond, Jean-Louis

    2012-09-15

    DrugBank (>6000 approved and experimental drugs) was analyzed using molecular quantum numbers (MQNs), which are 42 integer value descriptors of molecular structure counting atoms, bonds, polar groups and topological features. Principal component analysis of MQN-space showed that drugs differ mostly by size (PC1, 67% variance) and structural rigidity and polarity (PC2, 18% variance). Twenty-eight groups of target specific drugs were recovered by proximity sorting in MQN-space as efficiently as by substructure fingerprint (SF) similarity, but in different order allowing for lead-hopping relationships not seen in SF similarity. Clustering by MQN- or SF-similarity produced very different types of clusters. Each of the 28 drug groups spread over different clusters in both MQN- and SF-clustering, and most clusters contained drugs from different target specific groups, showing that structure-based classifications only partially overlap with bioactivity. An MQN-browsable version of DrugBank is available at www.gdb.unibe.ch. PMID:22465859

  3. Unexpected Giant-Gap Quantum Spin Hall Insulator in Chemically Decorated Plumbene Monolayer

    PubMed Central

    Zhao, Hui; Zhang, Chang-wen; Ji, Wei-xiao; Zhang, Run-wu; Li, Sheng-shi; Yan, Shi-shen; Zhang, Bao-min; Li, Ping; Wang, Pei-ji

    2016-01-01

    Quantum spin Hall (QSH) effect of two-dimensional (2D) materials features edge states that are topologically protected from backscattering by time-reversal symmetry. However, the major obstacles to the application for QSH effect are the lack of suitable QSH insulators with a large bulk gap. Here, we predict a novel class of 2D QSH insulators in X-decorated plumbene monolayers (PbX; X = H, F, Cl, Br, I) with extraordinarily giant bulk gaps from 1.03 eV to a record value of 1.34 eV. The topological characteristic of PbX mainly originates from s-px,y band inversion related to the lattice symmetry, while the effect of spin-orbital coupling (SOC) is only to open up a giant gap. Their QSH states are identified by nontrivial topological invariant Z2 = 1, as well as a single pair of topologically protected helical edge states locating inside the bulk gap. Noticeably, the QSH gaps of PbX are tunable and robust via external strain. We also propose high-dielectric-constant BN as an ideal substrate for the experimental realization of PbX, maintaining its nontrivial topology. These novel QSH insulators with giant gaps are a promising platform to enrich topological phenomena and expand potential applications at high temperature. PMID:26833133

  4. Tight-binding quantum chemical molecular dynamics simulations for the elucidation of chemical reaction dynamics in SiC etching with SF6/O2 plasma.

    PubMed

    Ito, Hiroshi; Kuwahara, Takuya; Kawaguchi, Kentaro; Higuchi, Yuji; Ozawa, Nobuki; Kubo, Momoji

    2016-03-21

    We used our etching simulator [H. Ito et al., J. Phys. Chem. C, 2014, 118, 21580-21588] based on tight-binding quantum chemical molecular dynamics (TB-QCMD) to elucidate SiC etching mechanisms. First, the SiC surface is irradiated with SF5 radicals, which are the dominant etchant species in experiments, with the irradiation energy of 300 eV. After SF5 radicals bombard the SiC surface, Si-C bonds dissociate, generating Si-F, C-F, Si-S, and C-S bonds. Then, etching products, such as SiS, CS, SiFx, and CFx (x = 1-4) molecules, are generated and evaporated. In particular, SiFx is the main generated species, and Si atoms are more likely to vaporize than C atoms. The remaining C atoms on SiC generate C-C bonds that may decrease the etching rate. Interestingly, far fewer Si-Si bonds than C-C bonds are generated. We also simulated SiC etching with SF3 radicals. Although the chemical reaction dynamics are similar to etching with SF5 radicals, the etching rate is lower. Next, to clarify the effect of O atom addition on the etching mechanism, we also simulated SiC etching with SF5 and O radicals/atoms. After bombardment with SF5 radicals, Si-C bonds dissociate in a similar way to the etching without O atoms. In addition, O atoms generate many C-O bonds and COy (y = 1-2) molecules, inhibiting the generation of C-C bonds. This indicates that O atom addition improves the removal of C atoms from SiC. However, for a high O concentration, many C-C and Si-Si bonds are generated. When the O atoms dissociate the Si-C bonds and generate dangling bonds, the O atoms terminate only one or two dangling bonds. Moreover, at high O concentrations there are fewer S and F atoms to terminate the dangling bonds than at low O concentration. Therefore, few dangling bonds of dissociated Si and C atoms are terminated, and they form many Si-Si and C-C bonds. Furthermore, we propose that the optimal O concentration is 50-60% because both Si and C atoms generate many etching products producing fewer C

  5. Quantum chemical study and infrared spectroscopy of hydrogen-bonded CHCl3-NH3 in the gas phase

    NASA Astrophysics Data System (ADS)

    Hippler, Michael

    2007-08-01

    Molecular association of chloroform with ammonia is studied by high-level quantum chemical calculations including correlated MP2 and CCSD(T) calculations with basis sets up to6-311++G(d,p) and counterpoise corrected energies, geometries, and frequencies. The calculations predict an eclipsed hydrogen-bonded complex of C3v symmetry (ΔE0=-15.07kJmol-1) with 225.4pm intermolecular CH⋯N distance. Intermolecular interactions are analysed by Kitaura-Morokuma [Int. J. Quantum Chem. 10, 325 (1976)] interaction energy decomposition. Compared to the monomer, the C-H bond is elongated, and the CH-stretching fundamental shifts to lower wave numbers and has a marked ˜340-fold increase of its intensity. Based on these predictions, the complex is observed by infrared spectroscopy in the gas phase at room temperature. A subtraction procedure isolates its spectrum, and a dilution series confirms the presence of a 1:1 complex. The CHCl3⋯NH3 complex has an experimental -17.5cm-1 shift of its CH-stretching vibration, and CDCl3⋯NH3 a -12.5cm-1 shift of the CD-stretching vibration. After a deperturbation of the CH-stretching/bending mode Fermi resonance system, this indicates a "redshifting" or more appropriately, a "C-H elongating" hydrogen bond in agreement with the ab initio calculations. An estimate of the complex concentration gives the equilibrium constant Kp=0.024 (pθ=105Pa ) at 295K for the dimerization, providing one of the few examples where a hydrogen-bonded gas phase complex at room temperature could be quantitatively studied by infrared spectroscopy.

  6. A versatile phenomenological model for the S-shaped temperature dependence of photoluminescence energy for an accurate determination of the exciton localization energy in bulk and quantum well structures

    NASA Astrophysics Data System (ADS)

    Dixit, V. K.; Porwal, S.; Singh, S. D.; Sharma, T. K.; Ghosh, Sandip; Oak, S. M.

    2014-02-01

    Temperature dependence of the photoluminescence (PL) peak energy of bulk and quantum well (QW) structures is studied by using a new phenomenological model for including the effect of localized states. In general an anomalous S-shaped temperature dependence of the PL peak energy is observed for many materials which is usually associated with the localization of excitons in band-tail states that are formed due to potential fluctuations. Under such conditions, the conventional models of Varshni, Viña and Passler fail to replicate the S-shaped temperature dependence of the PL peak energy and provide inconsistent and unrealistic values of the fitting parameters. The proposed formalism persuasively reproduces the S-shaped temperature dependence of the PL peak energy and provides an accurate determination of the exciton localization energy in bulk and QW structures along with the appropriate values of material parameters. An example of a strained InAs0.38P0.62/InP QW is presented by performing detailed temperature and excitation intensity dependent PL measurements and subsequent in-depth analysis using the proposed model. Versatility of the new formalism is tested on a few other semiconductor materials, e.g. GaN, nanotextured GaN, AlGaN and InGaN, which are known to have a significant contribution from the localized states. A quantitative evaluation of the fractional contribution of the localized states is essential for understanding the temperature dependence of the PL peak energy of bulk and QW well structures having a large contribution of the band-tail states.

  7. Quantum chemical assessment of the binding energy of CuO+

    NASA Astrophysics Data System (ADS)

    Rezabal, Elixabete; Gauss, Jürgen; Matxain, Jon M.; Berger, Robert; Diefenbach, Martin; Holthausen, Max C.

    2011-02-01

    We present a detailed theoretical investigation on the dissociation energy of CuO+, carried out by means of coupled cluster theory, the multireference averaged coupled pair functional (MR-ACPF) approach, diffusion quantum Monte Carlo (DMC), and density functional theory (DFT). At the respective extrapolated basis set limits, most post-Hartree-Fock approaches agree within a narrow error margin on a De value of 26.0 kcal mol-1 [coupled-cluster singles and doubles level augmented by perturbative triples corrections, CCSD(T)], 25.8 kcal mol-1 (CCSDTQ via the high accuracy extrapolated ab initio thermochemistry protocol), and 25.6 kcal mol-1 (DMC), which is encouraging in view of the disaccording data published thus far. The configuration-interaction based MR-ACPF expansion, which includes single and double excitations only, gives a slightly lower value of 24.1 kcal mol-1, indicating that large basis sets and triple excitation patterns are necessary ingredients for a quantitative assessment. Our best estimate for D0 at the CCSD(T) level is 25.3 kcal mol-1, which is somewhat lower than the latest experimental value (D0 = 31.1 ± 2.8 kcal mol-1; reported by the Armentrout group) [Int. J. Mass Spectrom. 182/183, 99 (1999)]. These highly correlated methods are, however, computationally very demanding, and the results are therefore supplemented with those of more affordable DFT calculations. If used in combination with moderately-sized basis sets, the M05 and M06 hybrid functionals turn out to be promising candidates for studies on much larger systems containing a [CuO]+ core.

  8. Quantum chemical computations, vibrational spectroscopic analysis and antimicrobial studies of 2,3-Pyrazinedicarboxylic acid

    NASA Astrophysics Data System (ADS)

    Beaula, T. Joselin; Packiavathi, A.; Manimaran, D.; Joe, I. Hubert; Rastogi, V. K.; Jothy, V. Bena

    2015-03-01

    Density Functional Theory (DFT) calculations at B3PW91 level with 6-311G (d) basis sets were carried out for 2,3-Pyrazinedicarboxylic acid (PDCA) to analyze in detail the equilibrium geometries and vibrational spectra. Calculations reveal that the optimized geometry closely resembles the experimental XRD data. Vibrational spectra were analyzed on the basis of potential energy distribution (PED) of each vibrational mode, which provides quantitative as well as qualitative interpretation of IR and Raman spectra. Information about size, shape, charge density distribution and site of chemical reactivity of the molecule were obtained by mapping electron density isosurface with the electrostatic potential surface (ESP). Based on optimized ground state geometries, NBO analysis was performed to study donor-acceptor (bond-antibond) interactions. TD-DFT analysis was also performed to calculate energies, oscillator strength of electronic singlet-singlet transitions and the absorption wavelengths. The 13C and 1H nuclear magnetic resonance (NMR) chemical shifts of the molecule in the ground state were calculated by gauge independent atomic orbital (GIAO) method and compared with the experimental values. PDCA was screened for its antimicrobial activity and found to exhibit antifungal and antibacterial effects. Molecular docking was also performed for the different receptors.

  9. Environment effects on the CO vibrational shifts in erbium complexes: a quantum chemical study.

    PubMed

    Ottonelli, Massimo; Musso, Gianfranco; Dellepiane, Giovanna

    2008-11-20

    The stability of lanthanide complexes and the efficiency of the energy transfer process, which makes these molecules interesting materials for technological applications, are correlated to the chemical environment surrounding the metal ion. In particular the efficiency depends on the relative position of the antenna (the ligand moiety that acts as photon absorption center) and the lanthanide ion (the emitting center), while the stability of the complex is correlated to the strength of the coordination between the rare earth and the ligands. For these reasons, knowledge of the structural properties of the complex is an interesting task to achieve. Since a large number of ligand structures hold the carboxylate group (COO(-)), which is used as an anchor for binding the antennae to the lanthanide ion, in this work we will show how the vibrational shifts of this group, induced by the interactions between the carboxylate moiety and the metal center of the lanthanide complex, can be used for obtaining in a simple way information on the structure of the chemical environment surrounding the lanthanide ion.

  10. Quantum chemical simulations of atomic layer deposition of metal oxides and metal nitrides

    NASA Astrophysics Data System (ADS)

    Xu, Ye

    Scaling of SiO2 gate dielectrics to extend the miniaturization of complementary metal oxide semiconductor (CMOS) devices in accordance with Moore's Law has resulted in unacceptable tunneling current leakage levels. The projection that this challenge could significantly limit CMOS performance has prompted the intense search for alternative gate dielectric materials that can achieve high capacitances with physically thicker films which minimize tunneling leakage current. Atomic layer deposition is an ideal deposition method for high-k films because it controls the film thickness with atomic layer precision and can achieve high film conformality and uniformity. We use density functional theory (DFT) to explore chemical reactions involved in ALD processes at the atomic level. We have investigated different metal precursors for ALD process. Compared to halides, metal alkylamides are more favorable on nitrided silicon surfaces and subsequent film growth. Likewise, hafnium alkylamide is more favorable than water to initiate the nucleation on hydrogen terminated silicon surfaces. For deposition on organic self-assembled monolayers, different end groups significantly affect the selectivity towards ALD reactions. The chemical mechanisms involved in ALD of hafnium nitride, aluminum nitride are developed which provide an understanding to the difficulty in producing oxygen free metal nitrides by ALD. By combining ALD of metal oxide and metal nitride, a new method for incorporating nitrogen into oxide films is proposed. In TMA and ozone reaction, it's found that by-product water can be a catalyzer for this reaction.

  11. Molecular structure, vibrational, electronic and thermal properties of 4-vinylcyclohexene by quantum chemical calculations.

    PubMed

    Nagabalasubramanian, P B; Periandy, S; Karabacak, Mehmet; Govindarajan, M

    2015-06-15

    The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100cm(-1). The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated.

  12. Quantum chemical computations, vibrational spectroscopic analysis and antimicrobial studies of 2,3-Pyrazinedicarboxylic acid.

    PubMed

    Beaula, T Joselin; Packiavathi, A; Manimaran, D; Joe, I Hubert; Rastogi, V K; Jothy, V Bena

    2015-03-01

    Density Functional Theory (DFT) calculations at B3PW91 level with 6-311G (d) basis sets were carried out for 2,3-Pyrazinedicarboxylic acid (PDCA) to analyze in detail the equilibrium geometries and vibrational spectra. Calculations reveal that the optimized geometry closely resembles the experimental XRD data. Vibrational spectra were analyzed on the basis of potential energy distribution (PED) of each vibrational mode, which provides quantitative as well as qualitative interpretation of IR and Raman spectra. Information about size, shape, charge density distribution and site of chemical reactivity of the molecule were obtained by mapping electron density isosurface with the electrostatic potential surface (ESP). Based on optimized ground state geometries, NBO analysis was performed to study donor-acceptor (bond-antibond) interactions. TD-DFT analysis was also performed to calculate energies, oscillator strength of electronic singlet-singlet transitions and the absorption wavelengths. The (13)C and (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule in the ground state were calculated by gauge independent atomic orbital (GIAO) method and compared with the experimental values. PDCA was screened for its antimicrobial activity and found to exhibit antifungal and antibacterial effects. Molecular docking was also performed for the different receptors.

  13. Spectroscopic (vibrational, NMR and UV-vis.) and quantum chemical investigations on 4-hexyloxy-3-methoxybenzaldehyde

    NASA Astrophysics Data System (ADS)

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-01

    In this study, the 4-hexyloxy-3-methoxybenzaldehyde compound as one of the derivatives of vanillin which is a well known flavoring agent, C14H20O3, has been investigated by experimentally and extensively utilizing density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. In this context, the optimized geometry, vibrational frequencies, 1H and 13C NMR chemical shifts, UV-vis. (in gas phase and in methanol solvent) spectra, HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic parameters and atomic charges of 4-hexyloxy-3-methoxybenzaldehyde have been calculated. In addition, theoretically predicted IR, Raman and UV-vis. (in gas phase and in methanol solvent) spectra of the mentioned molecule have been constructed. The results calculated were compared with the experimental data.

  14. Spectroscopic (vibrational, NMR and UV-vis.) and quantum chemical investigations on 4-hexyloxy-3-methoxybenzaldehyde.

    PubMed

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-01

    In this study, the 4-hexyloxy-3-methoxybenzaldehyde compound as one of the derivatives of vanillin which is a well known flavoring agent, C14H20O3, has been investigated by experimentally and extensively utilizing density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. In this context, the optimized geometry, vibrational frequencies, (1)H and (13)C NMR chemical shifts, UV-vis. (in gas phase and in methanol solvent) spectra, HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic parameters and atomic charges of 4-hexyloxy-3-methoxybenzaldehyde have been calculated. In addition, theoretically predicted IR, Raman and UV-vis. (in gas phase and in methanol solvent) spectra of the mentioned molecule have been constructed. The results calculated were compared with the experimental data.

  15. Quantum chemical studies on (ZnO)n/(NiO)n heterostructured nanoclusters

    NASA Astrophysics Data System (ADS)

    Chandiramouli, R.; Sriram, S.; Balamurugan, D.

    2014-01-01

    The structural stability and electronic properties of (ZnO)n, (NiO)n, (ZnO)n/(NiO)n for n = (1 to 4) and 3D structures were studied using density functional theory. The geometrical optimisation of clusters implies that when the atoms in the cluster increase it leads to an increase in its stability. The stability drastically increases for the heterostructure of (ZnO)n/(NiO)n. The dipole moment of the clusters depends on the geometry of the cluster and it is found to be minimum for heterostructures representing more neutralised clusters. HOMO-LUMO energies, ionisation potential, electron affinity, chemical hardness, binding energies and vibrational analysis of different clusters are calculated and reported. The adsorption of CO on the different sites of nanoclusters are studied and discussed.

  16. Spectroscopic and quantum chemical electronic structure investigations of 3,4-dihydrocoumarin and 3-methylcoumarin.

    PubMed

    Arivazhagan, M; Kavitha, R; Subhasini, V P

    2014-09-15

    A complete vibrational analysis of 3,4-dihydrocoumarin and 3-methylcoumarin have been performed according to SQM force field method based on ab initio and DFT calculation 6-311++G(d,p) basis set and their frequencies are compared. The influences of carbon-oxygen bond and methyl group to the vibrational frequencies of the title compounds have been discussed. The pronounced decrease of the lone pair orbital occupancy and the molecular stabilization energy show the hyperconjugation interaction from the NBO analysis. Calculations of molecular orbital geometry show that the visible absorption maxima of DHC and 3MC correspond to the electron transition between frontier orbitals such as translation from HOMO to LUMO. Gauge-including atomic orbital (GIAO) 1H and 13C chemical shift calculations have been calculated. Area of high, neutral and low electrostatic potential is determined for DHC and 3MC. PMID:24813279

  17. Spectroscopic and quantum chemical electronic structure investigations of 3,4-dihydrocoumarin and 3-methylcoumarin

    NASA Astrophysics Data System (ADS)

    Arivazhagan, M.; Kavitha, R.; Subhasini, V. P.

    2014-09-01

    A complete vibrational analysis of 3,4-dihydrocoumarin and 3-methylcoumarin have been performed according to SQM force field method based on ab initio and DFT calculation 6-311++G(d,p) basis set and their frequencies are compared. The influences of carbon-oxygen bond and methyl group to the vibrational frequencies of the title compounds have been discussed. The pronounced decrease of the lone pair orbital occupancy and the molecular stabilization energy show the hyperconjugation interaction from the NBO analysis. Calculations of molecular orbital geometry show that the visible absorption maxima of DHC and 3MC correspond to the electron transition between frontier orbitals such as translation from HOMO to LUMO. Gauge-including atomic orbital (GIAO) 1H and 13C chemical shift calculations have been calculated. Area of high, neutral and low electrostatic potential is determined for DHC and 3MC.

  18. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1981-01-01

    A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

  19. Methods for directly determining the two-electron reduced density matrix with applications to quantum phase transitions and chemical reactions

    NASA Astrophysics Data System (ADS)

    Schwerdtfeger, Christine Ann

    An N-particle system can be described without approximation using a two-particle reduced density matrix (2-RDM) if the particles are indistinguishable and interact pairwise. If a 2-RDM is determined without using an N-particle wavefunction, the computational advantage of using a two-particle representation is realized. Directly minimizing the energy as a functional of the 2-RDM, however, does not yield a 2-RDM that describes an N -particle system (N-representable). In this thesis we discuss two approaches for determining approximately N-representable 2-RDMS without using wavefunctions. In the first approach, known as the variational 2-RDM method, we minimize the energy as a function of the 2-RDM while explicitly enforcing a subset of N-representability conditions on the 2-RDM to obtain a lower bound to the exact energy. We apply this approach to the strongly correlated quantum phase transition in the 1D transverse Ising model and demonstrate that compared to the exact solution, the variational 2-RDM method provides an accurate description of the Ising lattice and is an alternative tool for locating a quantum phase transition using only the ground electronic state. The second approach used in this work is the parametric 2-RDM method. The 2-RDM is parameterized using a reference 2-RDM and a subset of N-representability conditions. We apply the method to several isomerization reactions including those of oxywater, ammonia oxide, carbonic acid and diazene. Results obtained using the parametric 2-RDM method reproduce experimental results in predicting the equilibrium ratio of cis- to trans-carbonic acid isomers and describe the multireference transition state in the isomerization of diazene as well as multireference wavefunction methods. We extend the 2-RDM parameterization to describe electronic systems in arbitrary spin states and demonstrate similar accuracy at equilibrium and nonequilibrium geometries as was seen in describing singlet electronic states. Lastly, we

  20. Conformational landscape of diisopropyl ketone: quantum chemical calculations validated by microwave spectroscopy.

    PubMed

    Zhao, Yueyue; Mouhib, Halima; Stahl, Wolfgang

    2013-01-17

    We report on the gas-phase structure of the most abundant conformer of diisopropyl ketone, (CH(3))(2)HC-CO-CH(CH(3))(2), as observed by molecular beam Fourier transform microwave spectroscopy. The gas-phase structures of five conformers of diisopropyl ketone were optimized using ab initio calculations at the MP2/6-311++G(d,p) level of theory. The natures of the stationary points were verified using harmonic frequency calculations. The only conformer observed in the supersonic jet possesses C(2) symmetry and appears as an enantiomeric pair. From the microwave spectrum, a set of three highly accurate rotational constants, five centrifugal distortion constants, and three sextic centrifugal distortion constants were determined. The structure of the observed conformer was optimized again at different levels of theory using the HF, MP2, and B3LYP methods. The theoretical constants of the C(2) conformer were subsequently validated using the experimental constants. To understand the transitions of one conformer to the others, the isopropyl groups were rotated against each other. The resulting two-dimensional potential energy surface shows nicely the symmetry of the conformational landscape and also indicates the enantiomeric pairs of the conformers. The barriers to internal rotation of the methyl groups were determined to be 1052 and 905 cm(-1) at the MP2/6-311++G(d,p) and the B3LYP/6-311++G(d,p) levels, respectively. In agreement with the theoretical predictions, no internal rotation patterns could be observed in the microwave spectrum.

  1. The chemical mechanism of the limonene ozonolysis reaction in the SOA formation: A quantum chemistry and direct dynamic study

    NASA Astrophysics Data System (ADS)

    Sun, Tingli; Wang, Yudong; Zhang, Chenxi; Sun, Xiaomin; Wang, Wenxing

    2011-03-01

    The ozonolysis of limonene is one of the most important processes for secondary organic aerosol formation and a detailed understanding of the atmospheric chemistry of d-limonene is highly urgent. In this paper, the reaction of d-limonene with O 3 has been studied using high level molecular orbital theory. A detailed description of the possible ozonolysis mechanism in the presence of H 2O or NO is provided. The main products obtained are keto-limonene, limononic acid and 7OH-lim, which are low vapor pressure compounds. On the basis of the quantum chemical information, the direct dynamic calculation is performed and the rate constants are calculated over a temperature range of 200˜800 K using the transition state theory and canonical varitional transition state theory with small-curvature tunneling effect. The four-parameter formula of rate constants with the temperature is fitted and the lifetimes of the reaction species in the troposphere are estimated according to the rate constants, which can provide helpful information to the model simulation study.

  2. Multicolor Quantum Dot-Based Chemical Nose for Rapid and Array-Free Differentiation of Multiple Proteins.

    PubMed

    Xu, Qinfeng; Zhang, Yihong; Tang, Bo; Zhang, Chun-yang

    2016-02-16

    Nanomaterial-based differential sensors (e.g., chemical nose) have shown great potential for identification of multiple proteins because of their modulatable recognition and transduction capability but with the limitation of array separation, single-channel read-out, and long incubation time. Here, we develop a multicolor quantum dot (QD)-based multichannel sensing platform for rapid identification of multiple proteins in an array-free format within 1 min. A protein-binding dye of bromophenol blue (BPB) is explored as an efficient reversible quencher of QDs, and the mixture of BPB with multicolor QDs may generate the quenched QD-BPB complexes. The addition of proteins will disrupt the QD-BPB complexes as a result of the competitive protein-BPB binding, inducing the separation of BPB from the QDs and the generation of distinct fluorescence patterns. The multicolor patterns may be collected at a single-wavelength excitation and differentiated by a linear discriminant analysis (LDA). This multichannel sensing platform allows for the discrimination of ten proteins and seven cell lines with the fastest response rate reported to date, holding great promise for rapid and high-throughput medical diagnostics. PMID:26759896

  3. Prediction of hydrolysis pathways and kinetics for antibiotics under environmental pH conditions: a quantum chemical study on cephradine.

    PubMed

    Zhang, Haiqin; Xie, Hongbin; Chen, Jingwen; Zhang, Shushen

    2015-02-01

    Understanding hydrolysis pathways and kinetics of many antibiotics that have multiple hydrolyzable functional groups is important for their fate assessment. However, experimental determination of hydrolysis encounters difficulties due to time and cost restraint. We employed the density functional theory and transition state theory to predict the hydrolysis pathways and kinetics of cephradine, a model of cephalosporin with two hydrolyzable groups, two ionization states, two isomers and two nucleophilic attack directions. Results showed that the hydrolysis of cephradine at pH = 8.0 proceeds via opening of the β-lactam ring followed by intramolecular amidation. The predicted rate constants at different pH conditions are of the same order of magnitude as the experimental values, and the predicted products are confirmed by experiment. This study identified a catalytic role of the carboxyl group in the hydrolysis, and implies that the carboxyl group also plays a catalytic role in the hydrolysis of other cephalosporin and penicillin antibiotics. This is a first attempt to quantum chemically predict hydrolysis of an antibiotic with complex pathways, and indicates that to predict hydrolysis products under the environmental pH conditions, the variation of the rate constants for different pathways with pH should be evaluated.

  4. Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations.

    PubMed Central

    Cannon, W. R.; Briggs, J. M.; Shen, J.; McCammon, J. A.; Quiocho, F. A.

    1995-01-01

    Experimental studies on a bacterial sulfate receptor have indicated anomalous relative binding affinities for the mutations Ser130-->Cys,Ser130-->Gly, and Ser130-->Ala. The loss of affinity for sulfate in the former mutation was previously attributed to a greater steric effect on the part of the Cys side chain relative to the Ser side chain, whereas the relatively small loss of binding affinity for the latter two mutations was attributed to the loss of a single hydrogen bond. In this report we present quantum chemical and statistical thermodynamic studies of these mutations. Qualitative results from these studies indicate that for the Ser130-->Cys mutation the large decrease in binding affinity is in part caused by steric effects, but also significantly by the differential work required to polarize the Cys thiol group relative to the Ser hydroxyl group. The Gly mutant cobinds a water molecule in the same location as the Ser side chain resulting in a relatively small decrease in binding affinity. Results for the Ala mutant are in disagreement with experimental results but are likely to be limited by insufficient sampling of configuration space due to physical constraints applied during the simulation. PMID:7795522

  5. Exciton energy transfer-based quantum dot fluorescence sensing array: "chemical noses" for discrimination of different nucleobases.

    PubMed

    Liu, Jianbo; Li, Gui; Yang, Xiaohai; Wang, Kemin; Li, Li; Liu, Wei; Shi, Xing; Guo, Yali

    2015-01-20

    A novel exciton energy transfer-based fluorescence sensing array for the discrimination of different nucleobases was developed through target nucleobase-triggered self-assembly of quantum dots (QDs). Four QD nanoprobes with different ligand receptors, including mercaptoethylamine, N-acetyl-l-cysteine, 2-dimethyl-aminethanethiol, and thioglycolic acid, were created to detect and identify nucleobase targets. These QDs served as both selective recognition scaffolds and signal transduction elements for a biomolecule target. The extent of particle assembly, induced by the analyte-triggered self-assembly of QDs, led to an exciton energy transfer effect between interparticles that gave a readily detectable fluorescence quenching and distinct fluorescence response patterns. These patterns are characteristic for each nucleobase and can be quantitatively differentiated by linear discriminate analysis. Furthermore, a fingerprint-based barcode was established to conveniently discriminate the nucleobases. This pattern sensing was successfully used to identify nucleobase samples at unknown concentrations and five rare bases. In this "chemical noses" strategy, the robust characteristics of QD nanoprobes, coupled with the diversity of surface functionality that can be readily obtained using nanoparticles, provides a simple and label-free biosensing approach that shows great promise for biomedical applications. PMID:25495103

  6. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

    NASA Astrophysics Data System (ADS)

    Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

    2013-12-01

    Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

  7. Multicolor Quantum Dot-Based Chemical Nose for Rapid and Array-Free Differentiation of Multiple Proteins.

    PubMed

    Xu, Qinfeng; Zhang, Yihong; Tang, Bo; Zhang, Chun-yang

    2016-02-16

    Nanomaterial-based differential sensors (e.g., chemical nose) have shown great potential for identification of multiple proteins because of their modulatable recognition and transduction capability but with the limitation of array separation, single-channel read-out, and long incubation time. Here, we develop a multicolor quantum dot (QD)-based multichannel sensing platform for rapid identification of multiple proteins in an array-free format within 1 min. A protein-binding dye of bromophenol blue (BPB) is explored as an efficient reversible quencher of QDs, and the mixture of BPB with multicolor QDs may generate the quenched QD-BPB complexes. The addition of proteins will disrupt the QD-BPB complexes as a result of the competitive protein-BPB binding, inducing the separation of BPB from the QDs and the generation of distinct fluorescence patterns. The multicolor patterns may be collected at a single-wavelength excitation and differentiated by a linear discriminant analysis (LDA). This multichannel sensing platform allows for the discrimination of ten proteins and seven cell lines with the fastest response rate reported to date, holding great promise for rapid and high-throughput medical diagnostics.

  8. Mid-IR quantum cascade lasers as an enabling technology for a new generation of chemical analyzers for liquids

    NASA Astrophysics Data System (ADS)

    Lendl, B.; Reidl-Leuthner, C.; Ritter, W.

    2011-01-01

    This presentation introduces a chemical analyzer (The ERACHECK) which is based on quantum cascade laser technology for measuring oil-in-water. Using these mid-IR lasers, it was possible to develop a portable, robust and highly precise analyzer for the measurement of oil-in-water, a parameter which is vital in the petrochemical industry for process control and environmental analysis. The overall method employs a liquid-liquid extraction step of the aqueous sample using a cyclic, aliphatic hydrocarbon such as cyclohexane. Quantification is based on measurement of the C-H deformation vibrations of the extracted hydrocarbons in the cyclic extraction solvent. The developed method is linear from 0.5 - 2000 ppm of oil in water, with precisions well below 15% in terms of r.s.d for repeated measurements. The portability of the ERACHECK and its robustness has been key for its successful use on oil rigs as well as petrochemical production sites on land. The values provided by the ERACHECK correlate well with those obtained by the former CFC (Freon 113) based method for oil in water, which is no longer in use in industrialized countries due to the ozone depleting effect of the CFCs employed.

  9. Rotational Spectroscopy and Quantum Chemical Calculations of a Fruit Ester: the Microwave Spectrum of n-BUTYL Acetate

    NASA Astrophysics Data System (ADS)

    Attig, T.; Sutikdja, L. W.; Kannengiesser, R.; Stahl, W.; Kleiner, I.

    2013-06-01

    In the course of our studies on a number of aliphatic ester molecules and natural substances, the rotational spectrum of n-butyl acetate (CH_{3}-COO-C_4H_9) has been recorded for the first time in the 10-13.5 GHz frequency range, using the MB-FTMW spectrometer in Aachen, with an instrumental uncertainty of a few kHz for unblended lines. Three conformers were observed. The main conformer with C_{1} symmetry has a strong spectrum. The other two conformers have C_{s} and C_{1} symmetries. Their intensities are considerably weaker. The quantum chemical calculations of specific conformers were carried out at the MP2/6-311++G(d,p) level, and for the main conformer different levels of theory were calculated. To analyze the internal rotation of the acetyl methyl groups the codes XIAM (based on the Combined Axis Method) and BELGI (based on the Rho-Axis-Method) were used to model the large amplitude motion. The molecular structures of the three conformers were determined and the values of the experimental rotational constants were compared with those obtained by ab initio methods. For all conformers torsional barriers of approximately 100 cm^{-1} were found. This study is part of a larger project which aims at determining the lowest energy conformers and their structures of organic esters and ketones which are of interest for flavour or perfume synthetic applications. Project partly supported by the PHC PROCOPE 25059YB

  10. Chlorination of N-methylacetamide and amide-containing pharmaceuticals. Quantum-chemical study of the reaction mechanism.

    PubMed

    Šakić, Davor; Šonjić, Pavica; Tandarić, Tana; Vrček, Valerije

    2014-03-27

    Chlorination of amides is of utmost importance in biochemistry and environmental chemistry. Despite the huge body of data, the mechanism of reaction between amides and hypochlorous acid in aqueous environment remains unclear. In this work, the three different reaction pathways for chlorination of N-methylacetamide by HOCl have been considered: the one-step N-chlorination of the amide, the chlorination via O-chlorinated intermediate, and the N-chlorination of the iminol intermediate. The high-level quantum chemical G3B3 composite procedure, double-hybrid B2-PLYPD, B2K-PLYP methods, and global hybrid M06-2X and BMK methods have been employed. The calculated energy barriers have been compared to the experimental value of ΔG(#)298 ≈ 87 kJ/mol, which corresponds to reaction rate constant k(r) ≈ 0.0036 M(-1) s(-1). Only the mechanism in which the iminol form of N-methylacetamide reacts with HOCl is consistent (ΔG(#)298 = 87.3 kJ/mol at G3B3 level) with experimental results. The analogous reaction mechanism has been calculated as the most favorable pathway in the chlorination of small-sized amides and amide-containing pharmaceuticals: carbamazepine, acetaminophen, and phenytoin. We conclude that the formation of the iminol intermediate followed by its reaction with HOCl is the general mechanism of N-chlorination for a vast array of amides.

  11. Importance of cytochromes in cyclization reactions: quantum chemical study on a model reaction of proguanil to cycloguanil.

    PubMed

    Arfeen, Minhajul; Patel, Dhilon S; Abbat, Sheenu; Taxak, Nikhil; Bharatam, Prasad V

    2014-10-30

    Proguanil, an anti-malarial prodrug, undergoes cytochrome P450 catalyzed biotransformation to the pharmacologically active triazine metabolite (cycloguanil), which inhibits plasmodial dihydrofolate reductase. This cyclization is catalyzed by CYP2C19 and many anti-malarial lead compounds are being designed and synthesized to exploit this pathway. Quantum chemical calculations were performed using the model species (Cpd I for active species of cytochrome and N4-isopropyl-N6-methylbiguanide for proguanil) to elucidate the mechanism of the cyclization pathway. The overall reaction involves the loss of a water molecule, and is exothermic by approximately 55 kcal/mol, and involves a barrier of approximately 17 kcal/mol. The plausible reaction pathway involves the initial H-radical abstraction from the isopropyl group by Cpd I, followed by two alternative paths- (i) oxygen rebound to provide hydroxyl derivative and (ii) loss of additional H-radical to yield 1,3,5-triazatriene, which undergoes cyclization. This study helped in understanding the role of the active species of cytochromes in this important cyclization reaction.

  12. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers.

    PubMed

    Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

    2013-12-01

    Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

  13. Optical absorption measurements and quantum-chemical simulations of optical properties of novel fluoro derivatives of pyrazoloquinoline

    NASA Astrophysics Data System (ADS)

    Brik, M. G.; Kuznik, W.; Gondek, E.; Kityk, I. V.; Uchacz, T.; Szlachcic, P.; Jarosz, B.; Plucinski, K. J.

    2010-05-01

    The results of experimental research and quantum-chemical simulations of the absorption spectra of 1-(4-fluorophenyl)-3,4-diphenyl, 3-(4-fluorophenyl)-1,4-diphenyl, and 4-(4-fluorophenyl)-1,3-diphenyl-pyrazolo[3,4- b] quinoline are presented. Although the fluorine atom is located on different phenyl rings in these molecules, the absorption spectra do not differ significantly. Semi-empirical AM1, PM3 and RM1 methods, as well as ab initio ADF code-based calculations were used to optimize geometry, calculate the infrared and visible spectra of the afore mentioned compounds and analyze the molecular orbitals schemes. The results of calculations are in good agreement with the experimental data. It was also demonstrated that the positions of the fluorescence maxima depend significantly on the solvent (contrary to the absorption spectra), in which the molecules are embedded, which allows for manipulating with fluorescence properties of the synthesized molecules by changing the solvent.

  14. Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO.

    PubMed

    Götze, Jan Philipp; Saalfrank, Peter

    2012-05-01

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO(2) carbon atom. This kinetic isotope effect α = k(12)/k(13) for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of (12)CO(2) compared to (13)CO(2). The latter is the dominant mode for the product formation at the transition state.

  15. Nitrogen-Containing Analog of Dibenzoylmethanate of Boron Difluoride: Luminescence, Structure, Quantum Chemical Modeling, and Delay Fluorescence.

    PubMed

    Fedorenko, Elena V; Тretyakova, Galina O; Mirochnik, Anatolii G; Beloliptsev, Anton Yu; Svistunova, Irina V; Sazhnikov, Viacheslav A; Atabekyan, Levon S

    2016-09-01

    Boron difluoride of 3-amino-1,3-diphenyl-2-propene-1-onate (1) has been synthesized and its crystal structure has been determined. The comparative studies of 1 and its oxygen analog 1,3-diphenyl-1,3-dionate (dibenzoylmethanate) of boron difluoride (2) have been performed using the methods of stationary and time-resolved spectroscopy and quantum chemical modeling. It was established that at the transition from solutions to crystals, a bathochromic shift of the spectra and a significant increase of luminescence intensity of 1 take place. The luminescent properties of solutions of 1 and 2 are similar. The peculiarities of crystal packings of 1 and 2 are responsible for differences in crystals luminescent properties. For crystals of 2, one observes the luminescence of J-aggregates and excimers, while for 1, in which a dimer is an elementary structural fragment, only the excimer luminescence is registered. A delayed excimer fluorescence of the P-type was observed for crystals of 1 and 2 at room temperature. The intensity of the delayed fluorescence of 1 is 300-fold higher than that of 2. Graphical Abstract Luminescence of J-aggregates and the formation of excimers in crystals of 1 and 2. PMID:27422696

  16. A QSAR for the Mutagenic Potencies of Twelve 2-Amino-trimethylimidazopyridine Isomers: Structural, Quantum Chemical,and Hydropathic Factors

    SciTech Connect

    Knize, M G; Hatch, F T; Tanga, M J; Lau, E V; Colvin, M E

    2005-04-23

    An isomeric series of heterocyclic amines related to one found in heated muscle meats was investigated for properties that predict their measured mutagenic potency. Eleven of the 12 possible 2-amino-trimethylimidazopyridine (TMIP) isomers were tested for mutagenic potency in the Ames/Salmonella test with bacterial strain TA98, and resulted in a 600-fold range in potency. Structural, quantum chemical and hydropathic data were calculated on the parent molecules and the corresponding nitrenium ions of all of the tested isomers to establish models for predicting the potency of the unknown isomer. The regression model accounting for the largest fraction of the total variance in mutagenic potency contains four predictor variables: dipole moment, a measure of the gap between amine LUMO and HOMO energies, percent hydrophilic surface, and energy of amine LUMO. The most important determinants of high mutagenic potency in these amines are: (1) a small dipole moment, (2) the combination of b-face ring fusion and N3-methyl group, and (3) a lower calculated energy of the {pi} electron system. Based on predicted potency from the average of five models, the isomer not yet synthesized and tested is expected to have a mutagenic potency of 0.84 revertants/{micro}g in test strain TA98.

  17. Quantum chemical investigation of the primary thermal pyrolysis reactions of the sodium carboxylate group in a brown coal model.

    PubMed

    Li, Jian; Zhang, Baisheng; Zhang, Zhiqiang; Yan, Kefeng; Kang, Lixun

    2014-12-01

    The primary pyrolysis mechanisms of the sodium carboxylate group in sodium benzoate-used as a model compound of brown coal-were studied by performing quantum chemical computations using B3LYP and the CBS method. Various possible reaction pathways involving reactions such as unimolecular and bimolecular decarboxylation and decarbonylation, crosslinking, and radical attack in the brown coal matrix were explored. Without the participation of reactive radicals, unimolecular decarboxylation to release CO2 was calculated to be the most energetically favorable primary reaction pathway at the B3LYP/6-311+G (d, p) level of theory, and was also found to be more energetically favorable than decarboxylation of an carboxylic acid group. When CBS-QBS results were included, crosslinking between the sodium carboxylate group and the carboxylic acid and the decarboxylation of the sodium carboxylate group (catalyzed by the phenolic hydroxyl group) were found to be possible; this pathway competes with unimolecular decarboxylation of the sodium carboxylate group. Provided that H and CH3 radicals are present in the brown coal matrix and can access the sodium carboxylate group, accelerated pyrolysis of the sodium carboxylate group becomes feasible, leading to the release of an Na atom or an NaCO2 radical at the B3LYP/6-311+G (d, p) or CBS-QB3 level of theory, respectively.

  18. The calculation of polar surface area from first principles: an application of quantum chemical topology to drug design.

    PubMed

    Bytheway, Ian; Darley, Michael G; Popelier, Paul L A

    2008-03-01

    The calculation of polar surface areas (PSA) from the electron density using quantum chemical topology (QCT) and a newly developed algorithm to determine isodensity surface areas is described. PSA values were calculated from the atomic partitioning of B3LYP/6-311G* wavefunctions and the results described herein represent the first application of this new algorithm. PSA values were calculated for forty drugs and compared to the topological polar surface area (TPSA) and those calculated by the QikProp program. Oral bioavailabilities predicted from the QCT PSA values for a subset of twenty drugs (the Palm set) were similar to those predicted by the dynamic polar surface area (DPSA) and in general, are in agreement with the observed values. Overall, PSA values obtained from QCT were generally similar to the DPSA, TPSA, and QikProp values, though differences in fragment contributions were found, with nitrogen-bearing functional groups showing the largest variation between methods. Differences between methods showed how the calculation of the PSA is dependent on the method used and, therefore, judicious application of the upper limits used in the prediction of oral bioavailability is warranted. These results also indicate that, because of the differences in the way PSA values are calculated, values from the different methods should not be used interchangeably.

  19. Understanding ground- and excited-state properties of perylene tetracarboxylic acid bisimide crystals by means of quantum chemical computations.

    PubMed

    Zhao, Hong-Mei; Pfister, Johannes; Settels, Volker; Renz, Manuel; Kaupp, Martin; Dehm, Volker C; Würthner, Frank; Fink, Reinhold F; Engels, Bernd

    2009-11-01

    Quantum chemical protocols explaining the crystal structures and the visible light absorption properties of 3,4:9,10-perylene tetracarboxylic acid bisimide (PBI) derivates are proposed. Dispersion-corrected density functional theory has provided an intermolecular potential energy of PBI dimers showing several energetically low-lying minima, which corresponds well with the packing of different PBI dyes in the solid state. While the dispersion interaction is found to be crucial for the binding strength, the minimum structures of the PESs are best explained by electrostatic interactions. Furthermore, a method is introduced, which reproduces the photon energies at the absorption maxima of PBI pigments within 0.1 eV. It is based on time-dependent Hartree-Fock (TD-HF) excitation energies calculated for PBI dimers with the next-neighbor arrangement in the pigment and incorporates crystal packing effects. This success provides clear evidence that the electronically excited states, which determine the color of these pigments, have no significant charge-transfer character. The developed protocols can be applied in a routine manner to understand and to predict the properties of such pigments, which are important materials for organic solar cells and (opto-)electronic devices.

  20. Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase.

    PubMed

    Siegbahn, Per E M; Shestakov, Alexander F

    2005-07-15

    The catalytic mechanism of molybdenum containing CO dehydrogenase has been studied using hybrid DFT methods with quite large chemical models. The recent high-resolution X-ray structure, showing the surprising presence of copper linked to molybdenum, was used as a starting point. A pathway was initially found with a low barrier for C-O bond formation and CO2 release. However, this pathway did not include the formation of any S-CO2 species, which had been suggested by experiments with an n-butylisocyanide inhibitor. When these SCO2 structures were studied they were found to lead to deep minima, making CO2 release much more difficult. A large effort was spent, including investigations of other spin states, varying the number of protons and electrons, adding water, etc., until a plausible pathway for S-C bond cleavage was found. In this pathway a water molecule is inserted in between molybdenum and the SCO2 group. Full catalytic cycles, including electron and proton transfers, are constructed both with and without S-C bond formation. When these pathways are extended to two full catalytic cycles it can be understood why the formation of the S-C bond actually makes catalysis faster, even though the individual step of CO2 release becomes much more difficult. These results agree well with experimental findings. PMID:15834924