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.
Machine learning of parameters for accurate semiempirical quantum chemical calculations
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
Machine learning of parameters for accurate semiempirical quantum chemical calculations
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 C_{7}H_{10}O_{2}, 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.
Chemically accurate description of aromatic rings interaction using quantum Monte Carlo
NASA Astrophysics Data System (ADS)
Azadi, Sam
We present an accurate study of interactions between benzene molecules using wave function based quantum Monte Carlo (QMC) methods. We compare our QMC results with density functional theory (DFT) using various van der Waals (vdW) functionals. This comparison enables us to tune vdW functionals. We show that highly optimizing the wave function and introducing more dynamical correlation into the wave function are crucial to calculate the weak chemical binding energy between benzene molecules. The good agreement among our results, experiments and quantum chemistry methods, is an important sign of the capability of the wave function based QMC methods to provide accurate description of very weak intermolecular interactions based on vdW dispersive forces.
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
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.
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.
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.
Accurate Evaluation of Quantum Integrals
NASA Technical Reports Server (NTRS)
Galant, David C.; Goorvitch, D.
1994-01-01
Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.
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
Accurate calculation of (31)P NMR chemical shifts in polyoxometalates.
Pascual-Borràs, Magda; López, Xavier; Poblet, Josep M
2015-04-14
We search for the best density functional theory strategy for the determination of (31)P nuclear magnetic resonance (NMR) chemical shifts, δ((31)P), in polyoxometalates. Among the variables governing the quality of the quantum modelling, we tackle herein the influence of the functional and the basis set. The spin-orbit and solvent effects were routinely included. To do so we analysed the family of structures α-[P2W18-xMxO62](n-) with M = Mo(VI), V(V) or Nb(V); [P2W17O62(M'R)](n-) with M' = Sn(IV), Ge(IV) and Ru(II) and [PW12-xMxO40](n-) with M = Pd(IV), Nb(V) and Ti(IV). The main results suggest that, to date, the best procedure for the accurate calculation of δ((31)P) in polyoxometalates is the combination of TZP/PBE//TZ2P/OPBE (for NMR//optimization step). The hybrid functionals (PBE0, B3LYP) tested herein were applied to the NMR step, besides being more CPU-consuming, do not outperform pure GGA functionals. Although previous studies on (183)W NMR suggested that the use of very large basis sets like QZ4P were needed for geometry optimization, the present results indicate that TZ2P suffices if the functional is optimal. Moreover, scaling corrections were applied to the results providing low mean absolute errors below 1 ppm for δ((31)P), which is a step forward in order to confirm or predict chemical shifts in polyoxometalates. Finally, via a simplified molecular model, we establish how the small variations in δ((31)P) arise from energy changes in the occupied and virtual orbitals of the PO4 group. PMID:25738630
An accurate and simple quantum model for liquid water.
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
Quantum logics and chemical kinetics
NASA Astrophysics Data System (ADS)
Ivanov, C. I.
1981-06-01
A statistical theory of chemical kinetics is presented based on the quantum logical concept of chemical observables. The apparatus of Boolean algebra B is applied for the construction of appropriate composition polynomials referring to any stipulated arrangement of the atomic constituents. A physically motivated probability measure μ( F) is introduced on the field B of chemical observables, which considers the occurrence of the yes response of a given F ɛ B. The equations for the time evolution of the species density operators and the master equations for the corresponding number densities are derived. The general treatment is applied to a superposition of elementary substitution reactions (AB) α + C ⇄ (AC) β + B. The expressions for the reaction rate coefficients are established.
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.
Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions
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.
Accurate ab initio energy gradients in chemical compound space.
Anatole von Lilienfeld, O
2009-10-28
Analytical potential energy derivatives, based on the Hellmann-Feynman theorem, are presented for any pair of isoelectronic compounds. Since energies are not necessarily monotonic functions between compounds, these derivatives can fail to predict the right trends of the effect of alchemical mutation. However, quantitative estimates without additional self-consistency calculations can be made when the Hellmann-Feynman derivative is multiplied with a linearization coefficient that is obtained from a reference pair of compounds. These results suggest that accurate predictions can be made regarding any molecule's energetic properties as long as energies and gradients of three other molecules have been provided. The linearization coefficent can be interpreted as a quantitative measure of chemical similarity. Presented numerical evidence includes predictions of electronic eigenvalues of saturated and aromatic molecular hydrocarbons. PMID:19894922
Accurate energies of the He atom with undergraduate quantum mechanics
NASA Astrophysics Data System (ADS)
Massé, Robert C.; Walker, Thad G.
2015-08-01
Estimating the energies and splitting of the 1s2s singlet and triplet states of helium is a classic exercise in quantum perturbation theory but yields only qualitatively correct results. Using a six-line computer program, the 1s2s energies calculated by matrix diagonalization using a seven-state basis improve the results to 0.4% error or better. This is an effective and practical illustration of the quantitative power of quantum mechanics, at a level accessible to undergraduate students.
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
Victora, Andrea; Möller, Heiko M; Exner, Thomas E
2014-12-16
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 (r(2)) 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
Chemical accuracy from quantum Monte Carlo for the benzene dimer
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.
Chemical accuracy from quantum Monte Carlo for the benzene dimer.
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
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 ...
Remote Chemical Detection using Quantum Cascade Lasers
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
Fast and accurate predictions of covalent bonds in chemical space.
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
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
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.
Spectroscopic and quantum chemical studies of isocytosine
Tulub, A.A.; Semenov, S.G.; Stetsenko, A.I.; Yudovich, E.E.
1988-07-01
The methods of electronic and vibrational (IR) spectroscopy were used to study the spectral properties of isocytosine in H/sub 2/O, D/sub 2/O, chloroform, and hexane in a wide concentration interval. Quantum chemical calculations of tautomeric forms and dimers of isocytosine were carried out. The bands of the calculated and experimental spectra were assigned. The results of the quantum calculations were compared with the experimental data. The spectral bands were classified according to the type of tautomer or dimer to which they belong.
Danshita, Ippei; Polkovnikov, Anatoli
2010-09-01
We study the quantum dynamics of supercurrents of one-dimensional Bose gases in a ring optical lattice to verify instanton methods applied to coherent macroscopic quantum tunneling (MQT). We directly simulate the real-time quantum dynamics of supercurrents, where a coherent oscillation between two macroscopically distinct current states occurs due to MQT. The tunneling rate extracted from the coherent oscillation is compared with that given by the instanton method. We find that the instanton method is quantitatively accurate when the effective Planck's constant is sufficiently small. We also find phase slips associated with the oscillations.
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.
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.
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.
Chemical dynamics in the gas phase : quantum mechanics of chemical reactions.
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.
Chemical dynamics in the gas phase : quantum mechanics of chemical reactions.
Gray, S. K.
1999-07-02
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.
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.
Quantum dynamics of fast chemical reactions
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.
Ligand Affinities Estimated by Quantum Chemical Calculations.
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
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.
NASA Astrophysics Data System (ADS)
Garrison, Stephen L.
2005-07-01
The combination of molecular simulations and potentials obtained from quantum chemistry is shown to be able to provide reasonably accurate thermodynamic property predictions. Gibbs ensemble Monte Carlo simulations are used to understand the effects of small perturbations to various regions of the model Lennard-Jones 12-6 potential. However, when the phase behavior and second virial coefficient are scaled by the critical properties calculated for each potential, the results obey a corresponding states relation suggesting a non-uniqueness problem for interaction potentials fit to experimental phase behavior. Several variations of a procedure collectively referred to as quantum mechanical Hybrid Methods for Interaction Energies (HM-IE) are developed and used to accurately estimate interaction energies from CCSD(T) calculations with a large basis set in a computationally efficient manner for the neon-neon, acetylene-acetylene, and nitrogen-benzene systems. Using these results and methods, an ab initio, pairwise-additive, site-site potential for acetylene is determined and then improved using results from molecular simulations using this initial potential. The initial simulation results also indicate that a limited range of energies important for accurate phase behavior predictions. Second virial coefficients calculated from the improved potential indicate that one set of experimental data in the literature is likely erroneous. This prescription is then applied to methanethiol. Difficulties in modeling the effects of the lone pair electrons suggest that charges on the lone pair sites negatively impact the ability of the intermolecular potential to describe certain orientations, but that the lone pair sites may be necessary to reasonably duplicate the interaction energies for several orientations. Two possible methods for incorporating the effects of three-body interactions into simulations within the pairwise-additivity formulation are also developed. A low density
NASA Astrophysics Data System (ADS)
Ge, Rong-Chun; Hughes, Stephen
2015-11-01
We study the quantum dynamics of two quantum dots (QDs) or artificial atoms coupled through the fundamental localized plasmon of a gold nanorod resonator. We derive an intuitive and efficient time-local master equation, in which the effect of the metal nanorod is taken into consideration self-consistently using a quasinormal mode (QNM) expansion technique of the photon Green function. Our efficient QNM technique offers an alternative and more powerful approach over the standard Jaynes-Cummings model, where the radiative decay, nonradiative decay, and spectral reshaping effect of the electromagnetic environment is rigorously included in a clear and transparent way. We also show how one can use our approach to compliment the approximate Jaynes-Cummings model in certain spatial regimes where it is deemed to be valid. We then present a study of the quantum dynamics and photoluminescence spectra of the two plasmon-coupled QDs. We first explore the non-Markovian regime, which is found to be important only on the ultrashort time scale of the plasmon mode which is about 40 fs. For the field free evolution case of excited QDs near the nanorod, we demonstrate how spatially separated QDs can be effectively coupled through the plasmon resonance and we show how frequencies away from the plasmon resonance can be more effective for coherently coupling the QDs. Despite the strong inherent dissipation of gold nanoresonators, we show that qubit entanglements as large as 0.7 can be achieved from an initially separate state, which has been limited to less than 0.5 in previous work for weakly coupled reservoirs. We also study the superradiance and subradiance decay dynamics of the QD pair. Finally, we investigate the rich quantum dynamics of QDs that are incoherently pumped, and study the polarization dependent behavior of the emitted photoluminescence spectrum where a double-resonance structure is observed due to the strong photon exchange interactions. Our general quantum plasmonics
Remote chemical sensing with quantum cascade lasers
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.
Remote chemical sensing with quantum cascade lasers
NASA Astrophysics Data System (ADS)
Harper, Warren W.; Strasburg, Jana D.
2004-09-01
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 retroreflector. 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 ~1x10-4 could be achieved with 5 seconds of data averaging, even under high turbulence conditions.
Approaching chemical accuracy with quantum Monte Carlo.
Petruzielo, F R; Toulouse, Julien; Umrigar, C J
2012-03-28
A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space. PMID:22462844
Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes
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.
Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes
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
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.
Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua
2015-01-13
We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207
Chemically accurate energy barriers of small gas molecules moving through hexagonal water rings.
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. PMID:27345929
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
Remote Chemical Sensing Using Quantum Cascade Lasers
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.
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
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.
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
NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.
Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua
2013-01-01
Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp. PMID:24376713
NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data
Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua
2013-01-01
Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp. PMID:24376713
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.
Neal, Stephen; Nip, Alex M; Zhang, Haiyan; Wishart, David S
2003-07-01
A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts--RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of approximately 20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (<1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Halpha), 0.980 (13Calpha), 0.996 (13Cbeta), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http
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.
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).
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.
Yildiz, Dilan; Bozkaya, Uğur
2016-01-30
The extended Koopmans' theorem (EKT) provides a straightforward way to compute ionization potentials and electron affinities from any level of theory. Although it is widely applied to ionization potentials, the EKT approach has not been applied to evaluation of the chemical reactivity. We present the first benchmarking study to investigate the performance of the EKT methods for predictions of chemical potentials (μ) (hence electronegativities), chemical hardnesses (η), and electrophilicity indices (ω). We assess the performance of the EKT approaches for post-Hartree-Fock methods, such as Møller-Plesset perturbation theory, the coupled-electron pair theory, and their orbital-optimized counterparts for the evaluation of the chemical reactivity. Especially, results of the orbital-optimized coupled-electron pair theory method (with the aug-cc-pVQZ basis set) for predictions of the chemical reactivity are very promising; the corresponding mean absolute errors are 0.16, 0.28, and 0.09 eV for μ, η, and ω, respectively. PMID:26458329
Accurate dispensing of volatile reagents on demand for chemical reactions in EWOD chips
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
Accurate dispensing of volatile reagents on demand for chemical reactions in EWOD chips.
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. PMID:22825699
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. PMID:26696323
Forming NCO– in Dense Molecular Clouds: Possible Gas-Phase Chemical Paths From Quantum Calculations
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
Halogen bonded supramolecular capsules: a challenging test case for quantum chemical methods.
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
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.
H2 Adsorption in a Porous Crystal: Accurate First-Principles Quantum Simulation.
D'Arcy, Jordan H; Jordan, Meredith J T; Frankcombe, Terry J; Collins, Michael A
2015-12-17
A general method is presented for constructing, from ab initio quantum chemistry calculations, the potential energy surface (PES) for H2 absorbed in a porous crystalline material. The method is illustrated for the metal-organic framework material MOF-5. Rigid body quantum diffusion Monte Carlo simulations are used in the construction of the PES and to evaluate the quantum ground state of H2 in MOF-5, the zero-point energy, and the enthalpy of adsorption at 0 K. PMID:26322374
Limits and potentials of quantum chemical methods in modelling photosynthetic antennae.
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
Chemical application of diffusion quantum Monte Carlo
NASA Astrophysics Data System (ADS)
Reynolds, P. J.; Lester, W. A., Jr.
1983-10-01
The diffusion quantum Monte Carlo (QMC) method gives a stochastic solution to the Schroedinger equation. As an example the singlet-triplet splitting of the energy of the methylene molecule CH2 is given. The QMC algorithm was implemented on the CYBER 205, first as a direct transcription of the algorithm running on our 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 is discussed. Since CH2 has only eight electrons, most of the loops in this application are fairly short. The longest inner loops run over the set of atomic basis functions. The CPU time dependence obtained versus the number of basis functions is discussed and compared with that obtained from traditional quantum chemistry codes and that obtained from traditional computer architectures. Finally, preliminary work on restructuring the algorithm to compute the separate Monte Carlo realizations in parallel is discussed.
Remote Chemical Sensing Using Quantum Cascade Lasers
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.
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.
Chemically Accurate Simulation of a Polyatomic Molecule-Metal Surface Reaction.
Nattino, Francesco; Migliorini, Davide; Kroes, Geert-Jan; Dombrowski, Eric; High, Eric A; Killelea, Daniel R; Utz, Arthur L
2016-07-01
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
Chemically Accurate Simulation of a Polyatomic Molecule-Metal Surface Reaction
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
Quantum chemical parameters in QSAR: what do I use when?
Hickey, James P.
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.
Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions
NASA Astrophysics Data System (ADS)
Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán
2014-11-01
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.
Accelerating Wave Function Convergence in Interactive Quantum Chemical Reactivity Studies.
Mühlbach, Adrian H; Vaucher, Alain C; Reiher, Markus
2016-03-01
The inherently high computational cost of iterative self-consistent field (SCF) methods proves to be a critical issue delaying visual and haptic feedback in real-time quantum chemistry. In this work, we introduce two schemes for SCF acceleration. They provide a guess for the initial density matrix of the SCF procedure generated by extrapolation techniques. SCF optimizations then converge in fewer iterations, which decreases the execution time of the SCF optimization procedure. To benchmark the proposed propagation schemes, we developed a test bed for performing quantum chemical calculations on sequences of molecular structures mimicking real-time quantum chemical explorations. Explorations of a set of six model reactions employing the semi-empirical methods PM6 and DFTB3 in this testing environment showed that the proposed propagation schemes achieved speedups of up to 30% as a consequence of a reduced number of SCF iterations. PMID:26788887
Quantum and semiclassical theories of chemical reaction rates
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.
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.
NASA Astrophysics Data System (ADS)
Little, James L.; Cleven, Curtis D.; Brown, Stacy D.
2011-02-01
In many cases, an unknown to an investigator is actually known in the chemical literature. We refer to these types of compounds as "known unknowns." Chemical Abstracts Service (CAS) Registry is a particularly good source of these substances as it contains over 54 million entries. Accurate mass measurements can be used to query the CAS Registry by either molecular formulae or average molecular weights. Searching the database by the web-based version of SciFinder is the preferred approach when molecular formulae are available. However, if a definitive molecular formula cannot be ascertained, searching the database with STN Express by average molecular weights is a viable alternative. The results from either approach are refined by employing the number of associated references or minimal sample history as orthogonal filters. These approaches were shown to be successful in identifying "known unknowns" noted in LC-MS and even GC-MS analyses in our laboratory. In addition, they were demonstrated in the identification of a variety of compounds of interest to others.
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.
Asymmetric chemical reactions by polarized quantum beams
NASA Astrophysics Data System (ADS)
Takahashi, Jun-Ichi; Kobayashi, Kensei
One of the most attractive hypothesis for the origin of homochirality in terrestrial bio-organic compounds (L-amino acid and D-sugar dominant) is nominated as "Cosmic Scenario"; a chiral impulse from asymmetric excitation sources in space triggered asymmetric reactions on the surfaces of such space materials as meteorites or interstellar dusts prior to the existence of terrestrial life. 1) Effective asymmetric excitation sources in space are proposed as polarized quantum beams, such as circularly polarized light and spin polarized electrons. Circularly polarized light is emitted as synchrotron radiation from tightly captured electrons by intense magnetic field around neutron stars. In this case, either left-or right-handed polarized light can be observed depending on the direction of observation. On the other hand, spin polarized electrons is emitted as beta-ray in beta decay from radioactive nuclei or neutron fireballs in supernova explosion. 2) The spin of beta-ray electrons is longitudinally polarized due to parity non-conservation in the weak interaction. The helicity (the the projection of the spin onto the direction of kinetic momentum) of beta-ray electrons is universally negative (left-handed). For the purpose of verifying the asymmetric structure emergence in bio-organic compounds by polarized quantum beams, we are now carrying out laboratory simulations using circularly polarized light from synchrotron radiation facility or spin polarized electron beam from beta-ray radiation source. 3,4) The target samples are solid film or aqueous solution of racemic amino acids. 1) K.Kobayashi, K.Kaneko, J.Takahashi, Y.Takano, in Astrobiology: from simple molecules to primitive life; Ed. V.Basiuk; American Scientific Publisher: Valencia, 2008. 2) G.A.Gusev, T.Saito, V.A.Tsarev, A.V.Uryson, Origins Life Evol. Biosphere. 37, 259 (2007). 3) J.Takahashi, H.Shinojima, M.Seyama, Y.Ueno, T.Kaneko, K.Kobayashi, H.Mita, M.Adachi, M.Hosaka, M.Katoh, Int. J. Mol. Sci. 10, 3044
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.
Argudo, David; Bethel, Neville P; Marcoline, Frank V; Grabe, Michael
2016-07-01
Biological membranes deform in response to resident proteins leading to a coupling between membrane shape and protein localization. Additionally, the membrane influences the function of membrane proteins. Here we review contributions to this field from continuum elastic membrane models focusing on the class of models that couple the protein to the membrane. While it has been argued that continuum models cannot reproduce the distortions observed in fully-atomistic molecular dynamics simulations, we suggest that this failure can be overcome by using chemically accurate representations of the protein. We outline our recent advances along these lines with our hybrid continuum-atomistic model, and we show the model is in excellent agreement with fully-atomistic simulations of the nhTMEM16 lipid scramblase. We believe that the speed and accuracy of continuum-atomistic methodologies will make it possible to simulate large scale, slow biological processes, such as membrane morphological changes, that are currently beyond the scope of other computational approaches. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26853937
How accurately can the microcanonical ensemble describe small isolated quantum systems?
NASA Astrophysics Data System (ADS)
Ikeda, Tatsuhiko N.; Ueda, Masahito
2015-08-01
We numerically investigate quantum quenches of a nonintegrable hard-core Bose-Hubbard model to test the accuracy of the microcanonical ensemble in small isolated quantum systems. We show that, in a certain range of system size, the accuracy increases with the dimension of the Hilbert space D as 1 /D . We ascribe this rapid improvement to the absence of correlations between many-body energy eigenstates. Outside of that range, the accuracy is found to scale either as 1 /√{D } or algebraically with the system size.
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.
[Large scale quantum chemical calculation for drug discovery].
Kitaura, Kazuo
2011-01-01
Due to the increase in computer power and the development of computational methods, it becomes possible to perform quantum mechanical calculations of very large molecules such as proteins that were previously exclusively treated with classical force field methods. We have developed the fragment molecular orbital (FMO) method aimed at biomolecular applications. One of the important applications of the method is in structure-based drug design because it provides accurate descriptions of various non-bonded interactions between a protein and its ligand. In this article, the FMO method will be described as well as its applications to the analysis of protein-ligand binding. PMID:21804319
NASA Astrophysics Data System (ADS)
Javad Fahimi, Mohammad; Fathi, Davood; Ansari-Rad, Mehdi
2015-09-01
Electron transfer rate from quantum dot (QD) to metal oxide (MO) in quantum dot sensitized solar cells (QDSSCs) has an important role in the efficiency. In this work, we analyse the electron transfer rate from CdSe, CdS and CdTe QDs to TiO2, ZnO and SnO2 MOs by extending the related equations with considering various effects, based on the Marcus theory. In this regard, the effects of QD diameter, QD-MO spacing, the crystalline defects, temperature, and the reorganizational energy, on the electron transfer rate are investigated. The results show that, the maximum electron transfer rate is achieved for CdTe QD with the mentioned three MOs. Moreover, in order to direct the designer to reach the appropriate QDs-MOs combinations for obtaining the maximum electron transfer rate, the average electron transfer rate for various combinations is calculated. For the verification of simulation method, a part of work has been compared with the previous experimental and theoretical results, which indicates the correctness of our simulation algorithm.
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
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
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
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
Accurate Semilocal Density Functional for Condensed-Matter Physics and Quantum Chemistry.
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
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.
NASA Technical Reports Server (NTRS)
Mcgrath, W. R.; Richards, P. L.; Face, D. W.; Prober, D. E.; Lloyd, F. L.
1988-01-01
A systematic study of the gain and noise in superconductor-insulator-superconductor mixers employing Ta based, Nb based, and Pb-alloy based tunnel junctions was made. These junctions displayed both weak and strong quantum effects at a signal frequency of 33 GHz. The effects of energy gap sharpness and subgap current were investigated and are quantitatively related to mixer performance. Detailed comparisons are made of the mixing results with the predictions of a three-port model approximation to the Tucker theory. Mixer performance was measured with a novel test apparatus which is accurate enough to allow for the first quantitative tests of theoretical noise predictions. It is found that the three-port model of the Tucker theory underestimates the mixer noise temperature by a factor of about 2 for all of the mixers. In addition, predicted values of available mixer gain are in reasonable agreement with experiment when quantum effects are weak. However, as quantum effects become strong, the predicted available gain diverges to infinity, which is in sharp contrast to the experimental results. Predictions of coupled gain do not always show such divergences.
The Bondons: The Quantum Particles of the Chemical Bond
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
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
NASA Astrophysics Data System (ADS)
Luo, Ye; Sorella, Sandro
2014-03-01
We introduce a general and efficient method for the calculation of vibrational frequencies of electronic systems, ranging from molecules to solids. By performing damped molecular dynamics with ab initio forces, we show that quantum vibrational frequencies can be evaluated by diagonalizing the time averaged position-position or force-force correlation matrices, although the ionic motion is treated on the classical level within the Born-Oppenheimer approximation. The novelty of our approach is to evaluate atomic forces with QMC by means of a highly accurate and correlated variational wave function which is optimized simultaneously during the dynamics. QMC is an accurate and promising many-body technique for electronic structure calculation thanks to massively parallel computers. However, since infinite statistics is not feasible, property evaluation may be affected by large noise that is difficult to harness. Our approach controls the QMC stochastic bias systematically and gives very accurate results with moderate computational effort, namely even with noisy forces. We prove the accuracy and efficiency of our method on the water monomer[A. Zen et al., JCTC 9 (2013) 4332] and dimer. We are currently working on the challenging problem of simulating liquid water at ambient conditions.
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
NASA Astrophysics Data System (ADS)
Wong, Molly; Zhang, Da; Rong, John; Wu, Xizeng; Liu, Hong
2009-10-01
Our goal was to evaluate the error contributed by photon fluence measurements to the detective quantum efficiency (DQE) of an x-ray imaging system. The investigation consisted of separate error analyses for the exposure and spectrum measurements that determine the photon fluence. Methods were developed for each to determine the number of measurements required to achieve an acceptable error. A new method for calculating the magnification factor in the exposure measurements was presented and compared to the existing method. The new method not only produces much lower error at small source-to-image distances (SIDs) such as clinical systems, but is also independent of SID. The exposure and spectra results were combined to determine the photon fluence error contribution to the DQE of 4%. The error in this study is small because the measurements resulted from precisely controlled experimental procedures designed to minimize the error. However, these procedures are difficult to follow in clinical environments, and application of this method on clinical systems could therefore provide important insight into error reduction. This investigation was focused on the error in the photon fluence contribution to the DQE, but the error analysis method can easily be extended to a wide range of applications.
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).
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). PMID:23248981
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.
NASA Astrophysics Data System (ADS)
Halverson, Thomas; Poirier, Bill
2012-12-01
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003);, 10.1142/S0219633603000380 B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004);, 10.1063/1.1767511 B. Poirier and A. Salam, J. Chem. Phys. 121, 1704 (2004), 10.1063/1.1767512], 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).
NASA Astrophysics Data System (ADS)
Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul
2015-03-01
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 103-105 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.
Stabilized Quantum Cascade Lasers and Ultrasensitive Chemical Sensing
NASA Astrophysics Data System (ADS)
Taubman, Matthew S.
2003-03-01
Quantum Cascade Lasers (QCLs) are a relatively new type of semiconductor laser operating in the mid- to long-wave infrared. Being monopolar multilayered quantum well structures, they can be fabricated to operate anywhere in a 3 to 20 micron region. This makes them an ideal choice for infrared chemical sensing, a topic of great interest at present. The broad range of applications of this technology includes everything from environmental sensing to homeland security and the non-proliferation of weapons of mass destruction. In addition to a discussion of these new laser devices, we will show results of resent experiments, including frequency stabilization of QCLs down to a relative frequency of 5.6Hz. In this experiment we use two QCLs locked to two separate optical cavities, and we observe the heterodyne beat. A third control loop (in addition to the two for locking the lasers) is used to remove low frequency noise between the two cavity systems. We also present data from several different cavity-enhanced QCL chemical sensors demonstrating sensitivities down to the mid 10-11/cm/root(Hz).
A microwave and quantum chemical study of allyltrifluorosilane
NASA Astrophysics Data System (ADS)
Møllendal, H.; Guirgis, G. A.
2003-04-01
The structural and conformational properties of allytrifluorsilane, H 2CCH-CH 2-SiF 3, have been explored by microwave (MW) spectroscopy and high-level ab initio and density functional theory quantum chemical calculations. The microwave spectrum was investigated in the 18-62 GHz spectral regions. The a-type R-branch transitions of one conformer were assigned for the ground as well as for 10 vibrationally excited states. The CC-C-Si chain of atoms in this rotamer takes an anti-clinal ('skew') conformation, with a dihedral angle calculated to be 111.6° from the syn-periplanar (0°) conformation. The question whether a CC-C-Si syn-periplanar conformer exists as a high-energy form in the gas phase remains open. In most of the quantum chemical calculations this conformation is predicted to be a transition state. However, in the most advanced calculations (B3LYP/aug-cc-pVTZ level of theory) the syn-periplanar conformer is predicted to be a stable rotamer that is calculated to be 6.5 kJ/mol higher in energy than the anti-clinal form. Since there is no indication in the MW spectrum for the presence of high-energy form(s), it is concluded that the anti-clinal conformer is at least 4 kJ/mol more stable than any other hypothetical rotamer.
Response to “Accurate Risk-Based Chemical Screening Relies on Robust Exposure Estimates”
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
Zou, Lindong; Li, Jun; Wang, Hui; Ma, Jianyi; Guo, Hua
2015-07-16
Full-dimensional quantum dynamics studies of the photodetachment of HCO2(-) and DCO2(-) are reported using a wave-packet method on an accurate global potential energy surface of the neutral HOCO/HCO2 system. The calculated photoelectron spectra reproduced both the positions and widths of the main HCO2 and DCO2 peaks observed in experiment. Specifically, both the (2)A1 and (2)B2 resonance peaks of the neutral radicals were identified in our simulations thanks to the adiabatic PES that captures both the (2)A1 and (2)B2 minima. The narrow widths and isotope effect of the lowest resonances are indicative of tunneling-facilitated predissociation. Furthermore, the dissociation product CO2 was found to be excited in both its symmetric stretching and bending modes, which are coupled via a strong Fermi resonance, but rotationally cold, in good agreement with the recent photoelectron-photodetachment coincidence experiments. PMID:25607218
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).
Radiation and quantum chemical studies of chalcone derivatives.
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
Spectroscopic and quantum chemical studies on 4-acryloyl morpholine
NASA Astrophysics Data System (ADS)
Arjunan, V.; Rani, T.; Santhanalakshmi, K.; Mohan, S.
2011-09-01
Fourier transform infrared (FTIR) and FT-Raman spectra have been recorded and an extensive spectroscopic investigations have been carried out on 4-acryloyl morpholine (4AM). Theoretical quantum chemical studies have also been performed. From the ab initio and DFT analysis using HF, B3LYP and B3PW91 methods with 6-31G(d,p) and 6-311G++(d,p) basis sets the energies, structural, thermodynamical and vibrational characteristics of the compound were determined. The energy difference between the chair equatorial and chair axial conformers of 4AM have been calculated by density functional theory (DFT) method. The optimized geometrical parameters, theoretical wavenumbers and thermodynamic properties of the molecule are compared with the experimental values. The effect of acryloyl group on the characteristic frequencies of the morpholine ring has been analysed. The mixing of the fundamental modes with the help of potential energy distribution (PED) through normal co-ordinate analysis has been discussed.
Simulation of chemical isomerization reaction dynamics on a NMR quantum simulator.
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. PMID:21797586
NASA Astrophysics Data System (ADS)
Nakai, Hiromi; Ishikawa, Atsushi
2014-11-01
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 CO2 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.
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.
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
Quantum Chemical Study of the Thermochemical Properties of Organophosphorous Compounds.
Khalfa, A; Ferrari, M; Fournet, R; Sirjean, B; Verdier, L; Glaude, P A
2015-10-22
Organophosphorous compounds are involved in many toxic compounds such as fungicides, pesticides, or chemical warfare nerve agents. The understanding of the decomposition chemistry of these compounds in the environment is largely limited by the scarcity of thermochemical data. Because of the high toxicity of many of these molecules, experimental determination of their thermochemical properties is very difficult. In this work, standard gas-phase thermodynamic data, i.e., enthalpies of formation (ΔfH298°), standard entropies (S298°), and heat capacities (Cp°(T)), were determined using quantum chemical calculations and more specifically the CBS-QB3 composite method, which was found to be the best compromise between precision and calculation time among high accuracy composite methods. A large number of molecules was theoretically investigated, involving trivalent and pentavalent phosphorus atoms, and C, H, O, N, S, and F atoms. These data were used to propose 83 original groups, used in the semiempirical group contribution method proposed by Benson. Thanks to these latter group values, thermochemical properties of several nerve agents, common pesticides and herbicides have been evaluated. Bond dissociations energies (BDE), useful for the analysis the thermal stability of the compounds, were also determined in several molecules of interest. PMID:26434606
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.
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.
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.
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
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
Ren, Yinghui; Bian, Wensheng
2015-05-21
We present the first accurate quantum dynamics calculations of mode-specific tunneling splittings in a sequential double-hydrogen transfer process. This is achieved in the vinylidene-acetylene system, the simplest molecular system of this kind, and by large-scale parallel computations with an efficient theoretical scheme developed by us. In our scheme, basis functions are customized for the hydrogen transfer process; a 4-dimensional basis contraction strategy is combined with the preconditioned inexact spectral transform method; efficient parallel implementation is achieved. Mode-specific permutation tunneling splittings of vinylidene states are reported and tremendous mode-specific promotion effects are revealed; in particular, the CH2 rock mode enhances the ground-state splitting by a factor of 10(3). We find that the ground-state vinylidene has a reversible-isomerization time of 622 ps, much longer than all previous estimates. Our calculations also shed light on the importance of the deep intermediate well and vibrational excitation in the double-hydrogen transfer processes. PMID:26263255
Tabatabaei-Panah, Akram-Sadat; Jeddi-Tehrani, Mahmood; Ghods, Roya; Akhondi, Mohammad-Mehdi; Mojtabavi, Nazanin; Mahmoudi, Ahmad-Reza; Mirzadegan, Ebrahim; Shojaeian, Sorour; Zarnani, Amir-Hassan
2013-03-01
Here we introduce novel optical properties and accurate sensitivity of Quantum dot (QD)-based detection system for tracking the breast cancer marker, HER2. QD525 was used to detect HER2 using home-made HER2-specific monoclonal antibodies in fixed and living HER2(+) SKBR-3 cell line and breast cancer tissues. Additionally, we compared fluorescence intensity (FI), photostability and staining index (SI) of QD525 signals at different exposure times and two excitation wavelengths with those of the conventional organic dye, FITC. Labeling signals of QD525 in both fixed and living breast cancer cells and tissue preparations were found to be significantly higher than those of FITC at 460-495 nm excitation wavelengths. Interestingly, when excited at 330-385 nm, the superiority of QD525 was more highlighted with at least 4-5 fold higher FI and SI compared to FITC. Moreover, QDs exhibited exceptional photostability during continuous illumination of cancerous cells and tissues, while FITC signal faded very quickly. QDs can be used as sensitive reporters for in situ detection of tumor markers which in turn could be viewed as a novel approach for early detection of cancers. To take comprehensive advantage of QDs, it is necessary that their optimal excitation wavelength is employed. PMID:23212129
Jiang, Bin; Hu, Xixi; Lin, Sen; Xie, Daiqian; Guo, Hua
2015-09-28
Cobalt is a widely used catalyst for many heterogeneous reactions, including the Fischer-Tropsch (FT) process, which converts syngas (H2 and CO) to higher hydrocarbons. As a result, a better understanding of the key chemical steps on the Co surface, such as the dissociative chemisorption of H2 as an initial step of the FT process, is of fundamental importance. Here, we report an accurate full-dimensional global potential energy surface for the dissociative chemisorption of H2 on the rigid Co(0001) surface constructed from more than 3000 density functional theory points. The high-fidelity potential energy surface was obtained using the permutation invariant polynomial-neural network method, which preserves both the permutation symmetry of H2 and translational symmetry of the Co(0001) surface. The reaction path features a very low barrier on the top site. Full-dimensional quantum dynamical calculations provide insights into the dissociation dynamics and influence of the initial vibrational, rotational, and orientational degrees of freedom. PMID:26286861
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
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
Chemical Functionalisation and Photoluminescence of Graphene Quantum Dots.
Sekiya, Ryo; Uemura, Yuichiro; Naito, Hiroyoshi; Naka, Kensuke; Haino, Takeharu
2016-06-01
Chemical modification of graphene quantum dots (GQDs) can influence their physical and chemical properties; hence, the investigation of the effect of organic functional groups on GQDs is of importance for developing GQD-organic hybrid materials. Three peripherally functionalised GQDs having a third-generation dendritic wedge (GQD-2), long alkyl chains (GQD-3) and a polyhedral oligomeric silsesquioxane group (GQD-4) were prepared by the Cu(I) -catalysed Huisgen cycloaddition reaction of GQD-1 with organic azides. Cyclic voltammetry indicated that reduction occurred on the surfaces of GQD-1-4 and on the five-membered imide rings at the periphery, and this suggested that the functional groups distort the periphery by steric interactions between neighbouring functional groups. The HOMO-LUMO bandgaps of GQD-1-4 were estimated to be approximately 2 eV, and their low-lying LUMO levels (<-3.9 eV) were lower than that of phenyl-C61 -butyric acid methyl ester, an n-type organic semiconductor. The solubility of GQD-1-4 in organic solvents depends on the functional groups present. The functional groups likely cover the surfaces and periphery of the GQDs, and thus increase their affinity for solvent and avoid precipitation. Similar to GQD-2, both GQD-3 and GQD-4 emitted white light upon excitation at 360 nm. Size-exclusion chromatography demonstrated that white-light emission originates from the coexistence of differently sized GQDs that have different photoluminescence emission wavelengths. PMID:27115715
[Study of quantum-pharmacological chemical characteristics of quercetin].
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
Charge transport in conjugated materials: insight from quantum chemical calculations
NASA Astrophysics Data System (ADS)
Beljonne, David; Cornil, J. P.; Calbert, J. P.; Bredas, Jean-Luc
2001-06-01
The electronic structure of neutral and singly charged conjugated molecular clusters is investigated by means of quantum-chemical calculations. We first assess the influence of interchain interactions on the nature of the singly charged species (polarons) in organic conjugated polymers. In a two- chain model aggregate, the polaron is found to be delocalized over the two conjugated chains for short interchain separation. Such a delocalization strongly affects the geometric and electronic relaxation phenomena induced by charge injection, which in turn lead to a dramatic spectral redistribution of the linear absorption cross section. We then consider pentacene clusters built from the experimental crystal structure and compute the HOMO and LUMO bandwidths, which are decisive parameters for charge transport in the limiting case of band-like motion (i.e., complete delocalization of the excess charge over a large number of interacting molecules). Very large bandwidths are obtained, in agreement with the remarkable electron and hole charge-carrier mobilities reported recently for ultrahigh purity pentacene single crystals.
Quantum chemical study of the autoxidation of ascorbate.
Herrmann, Nils; Heinz, Norah; Dolg, Michael; Cao, Xiaoyan
2016-07-01
Reactions involved in the autoxidation of ascorbate have been investigated with quantum chemical first-principles and ab initio methods. Reaction energies and Gibbs energies of the reactions were calculated at the density functional theory level applying the gradient-corrected BP86 and the hybrid B3LYP functionals together with def2-TZVP basis sets. Results of single-point CC2, CCSD, and CCSD(T) calculations were used for calibration of the density functional theory data and show excellent agreement with the B3LYP values. Based on the Gibbs energy ascorbic acid AscH2 is found to be the energetically lowest species in aqueous solution, whereas the monoanion ascorbate AscH - is the most abundant one near pH = 7. Asc 2- was found to be the preferred reducing agent for autoxidation and oxidation processes. The results also support a metal-catalyzed synthesis of the reactive oxygen species H2 O2 according to a redox cycling mechanism proposed in literature. © 2016 Wiley Periodicals, Inc. PMID:27316823
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.
Quantum-chemical study of CHCl3-SO2 association.
Hippler, Michael
2005-11-22
CHCl(3)-SO(2) association is studied by high-level quantum-chemical calculations of stationary points of the dimer electronic potential-energy hypersurface, including correlated second-order Moller-Plesset and CCSD(T) calculations with basis sets up to 6-311++G(d,p). During geometry optimization, frequency, and energy calculations, a self-written computer code embedding the GAMESS ab initio program suite applies counterpoise correction of the basis set superposition error. A CH...O hydrogen-bonded complex (DeltaE(0)=-8.73 kJmol) with a 2.4 A intermolecular H...O distance and two very weak van der Waals complexes (DeltaE(0)=-3.78 and -2.94 kJmol) are located on the counterpoise-corrected potential-energy surface. The intermolecular interactions are characterized by Kitaura-Morokuma interaction energy decompositions and Mulliken electron population analyses. The unusual hydrogen bond is distinguished by a CH-bond contraction, a pronounced enhancement of the IR intensity and a shift to higher frequency ("blueshift") of the CH-stretching vibration compared to the CHCl(3) monomer. Spectroscopy and association in liquid solution is also discussed; our results provide an alternative explanation for features in the CH-stretching vibration spectrum of chloroform dissolved in liquid sulfur dioxide which have been attributed previously to an intermolecular Fermi resonance. PMID:16351260
Quantum-chemical study of CHCl3-SO2 association
NASA Astrophysics Data System (ADS)
Hippler, Michael
2005-11-01
CHCl3-SO2 association is studied by high-level quantum-chemical calculations of stationary points of the dimer electronic potential-energy hypersurface, including correlated second-order Møller-Plesset and CCSD(T) calculations with basis sets up to 6-311++G(d,p). During geometry optimization, frequency, and energy calculations, a self-written computer code embedding the GAMESS ab initio program suite applies counterpoise correction of the basis set superposition error. A CH ⋯O hydrogen-bonded complex (ΔE0=-8.73kJ/mol) with a 2.4Å intermolecular H ⋯O distance and two very weak van der Waals complexes (ΔE0=-3.78 and -2.94kJ /mol) are located on the counterpoise-corrected potential-energy surface. The intermolecular interactions are characterized by Kitaura-Morokuma interaction energy decompositions and Mulliken electron population analyses. The unusual hydrogen bond is distinguished by a CH-bond contraction, a pronounced enhancement of the IR intensity and a shift to higher frequency ("blueshift") of the CH-stretching vibration compared to the CHCl3 monomer. Spectroscopy and association in liquid solution is also discussed; our results provide an alternative explanation for features in the CH-stretching vibration spectrum of chloroform dissolved in liquid sulfur dioxide which have been attributed previously to an intermolecular Fermi resonance.
Chemically-mediated quantum criticality in NbFe2
Alam, Aftab; Johnson, Duane
2011-11-09
Laves-phase Nb{sub 1+c}Fe{sub 2-c} is a rare itinerant intermetallic compound exhibiting magnetic quantum criticality at c{sub cr} {approx} 1.5% Nb excess; its origin, and how alloying mediates it, remains an enigma. For NbFe{sub 2}, we show that an unconventional band critical point above the Fermi level E{sub F} explains most observations and that chemical alloying mediates access to this unconventional band critical point by an increase in E{sub F} with decreasing electrons (increasing %Nb), counter to rigid-band concepts. We calculate that E{sub F} enters the unconventional band critical point region for c{sub cr} > 1.5% Nb and by 1.74% Nb there is no Nb site-occupation preference between symmetry-distinct Fe sites, i.e., no electron-hopping disorder, making resistivity near constant as observed. At larger Nb (Fe) excess, the ferromagnetic Stoner criterion is satisfied.
Periodic quantum chemical studies on anhydrous and hydrated acid clinoptilolite.
Valdiviés Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M
2014-08-01
Periodic quantum chemistry methods as implemented in the crystal09 code were considered to study acid clinoptilolite (HEU framework type), both anhydrous and hydrated. The most probable location of acid sites and water molecules together with other structural details has been the object of particular attention. Calculations were performed at hybrid and pristine DFT levels of theory with a VDZP quality basis set in order to compare performances. It arises that PBE0 provides the best agreement with experimental data as concerns structural features and the most stable Al distribution in the framework. The role of the water molecule distribution in the stability of the systems, the most probable structure that they induce in the material, and their eventual influence on further chemical modification processes, such as dealumination, are discussed in detail. Results show that, apart from the usually considered interactions of water molecules with the zeolite framework, that is, a H-bond with Brönsted acid sites and coordination with framework Al as Lewis ones, it is necessary to consider cooperation of other weaker effects so as to fully understand the hydration effect in this kind of materials. PMID:24730675
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
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
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.
Chemical compass model for avian magnetoreception as a quantum coherent device.
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
Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.
Kruse, Holger; Mladek, Arnost; Gkionis, Konstantinos; Hansen, Andreas; Grimme, Stefan; Sponer, Jiri
2015-10-13
We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χOL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields. PMID:26574283
2014-01-01
Predicting the binding affinities of large sets of diverse molecules against a range of macromolecular targets is an extremely challenging task. The scoring functions that attempt such computational prediction are essential for exploiting and analyzing the outputs of docking, which is in turn an important tool in problems such as structure-based drug design. Classical scoring functions assume a predetermined theory-inspired functional form for the relationship between the variables that describe an experimentally determined or modeled structure of a protein–ligand complex and its binding affinity. The inherent problem of this approach is in the difficulty of explicitly modeling the various contributions of intermolecular interactions to binding affinity. New scoring functions based on machine-learning regression models, which are able to exploit effectively much larger amounts of experimental data and circumvent the need for a predetermined functional form, have already been shown to outperform a broad range of state-of-the-art scoring functions in a widely used benchmark. Here, we investigate the impact of the chemical description of the complex on the predictive power of the resulting scoring function using a systematic battery of numerical experiments. The latter resulted in the most accurate scoring function to date on the benchmark. Strikingly, we also found that a more precise chemical description of the protein–ligand complex does not generally lead to a more accurate prediction of binding affinity. We discuss four factors that may contribute to this result: modeling assumptions, codependence of representation and regression, data restricted to the bound state, and conformational heterogeneity in data. PMID:24528282
Optimization of an External Cavity Quantum Cascade Laser for Chemical Sensing Applications
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.
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.
Fast Infrared Chemical Imaging with a Quantum Cascade Laser
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
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
GaN quantum dots as optical transducers for chemical sensors
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.
NASA Technical Reports Server (NTRS)
Haugen, H. K.; Weitz, E.; Leone, S. R.
1985-01-01
Various techniques have been used to study photodissociation dynamics of the halogens and interhalogens. The quantum yields obtained by these techniques differ widely. The present investigation is concerned with a qualitatively new approach for obtaining highly accurate quantum yields for electronically excited states. This approach makes it possible to obtain an accuracy of 1 percent to 3 percent. It is shown that measurement of the initial transient gain/absorption vs the final absorption in a single time-resolved signal is a very accurate technique in the study of absolute branching fractions in photodissociation. The new technique is found to be insensitive to pulse and probe laser characteristics, molecular absorption cross sections, and absolute precursor density.
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.
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.
Quantum Hall effect on centimeter scale chemical vapor deposited graphene films
NASA Astrophysics Data System (ADS)
Shen, Tian; Wu, Wei; Yu, Qingkai; Richter, Curt A.; Elmquist, Randolph; Newell, David; Chen, Yong P.
2011-12-01
We report observations of well developed half integer quantum Hall effect on mono layer graphene films of 7 mm × 7 mm in size. The graphene films are grown by chemical vapor deposition on copper, then transferred to SiO2/Si substrates, with typical carrier mobilities ≈4000 cm2/Vs. The large size graphene with excellent quality and electronic homogeneity demonstrated in this work is promising for graphene-based quantum Hall resistance standards and can also facilitate a wide range of experiments on quantum Hall physics of graphene and practical applications exploiting the exceptional properties of graphene.
Quantum Hall effect on centimeter scale chemical vapor deposited graphene films
NASA Astrophysics Data System (ADS)
Shen, Tian; Wu, Wei; Yu, Qingkai; Richter, Curt; Elmquist, Randolph; Newell, David; Chen, Yong
2012-02-01
We report observations of well developed half integer quantum Hall effect on mono layer graphene films of 7 mm by 7 mm in size. The graphene films are grown by chemical vapor deposition on copper, then transferred to SiO2/Si substrates, with typical carrier mobilities 4000 cm^2/Vs. The large size graphene with excellent quality and electronic homogeneity demonstrated in this work is promising for graphene-based quantum Hall resistance standards, and can also facilitate a wide range of experiments on quantum Hall physics of graphene and practical applications exploiting the exceptional properties of graphene.
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.
Towards Quantum Simulation of Chemical Dynamics with Prethreshold Superconducting Qubits
NASA Astrophysics Data System (ADS)
Cook, A. W.; Stancil, P. C.; Geller, M.; You, Hao; Sornborger, A. T.
While large-scale, fault-tolerant quantum computing devices are still on the horizon, considerable activity has focused on quantum simulation (qs). While advances have been made in realizing both digital and analog qs, the former is still restricted by the need for fault-tolerant computational qubits. As an alternative, we are exploring the single excitation subspace (ses) approach which has the advantage of using today's prethreshold devices and can function as a schroedinger equation solver. One application of the ses method is the study of molecular collision problems. we are both developing efficient, optimized scattering approaches on classical computers and porting the method to an ses processor focusing on superconducting architectures. Issues related to propagator efficiency, multichannel potential averaging, and ehrenfest symmetrization have been explored. Results from classical calculations and simulations of qs for ion-atom collisions will be presented.
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.
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.
NASA Astrophysics Data System (ADS)
Hermann, R.; Naumov, S.; Mahalaxmi, G. R.; Brede, O.
2000-07-01
The deprotonation kinetics of phenol-type radical cations, formed via a very efficient electron transfer in the pulse radiolysis of non-polar solutions, for example n-chlorobutane, is governed mainly by electronic effects due to the nature of the phenol substituents, whereas steric effects are of minor importance; thiophenols, which are sulphur analogues of phenols, exhibit a similar behavior. Comparative quantum chemical calculations show that the calculated spin densities at the hetero atoms correlate well with the experimentally determined radical cation lifetimes. Not only the Density Functional Theory (DTF) B3LYP but also the semiempirical quantum chemical model PM3 can be applied for the open shell systems mentioned.
NASA Astrophysics Data System (ADS)
Bačić, Z.; Kress, J. D.; Parker, G. A.; Pack, R. T.
1990-02-01
Accurate 3D coupled channel calculations for total angular momentum J=0 for the reaction F+H2→HF+H using a realistic potential energy surface are analyzed. The reactive scattering is formulated using the hyperspherical (APH) coordinates of Pack and Parker. The adiabatic basis functions are generated quite efficiently using the discrete variable representation method. Reaction probabilities for relative collision energies of up to 17.4 kcal/mol are presented. To aid in the interpretation of the resonances and quantum structure observed in the calculated reaction probabilities, we analyze the phases of the S matrix transition elements, Argand diagrams, time delays and eigenlifetimes of the collision lifetime matrix. Collinear (1D) and reduced dimensional 3D bending corrected rotating linear model (BCRLM) calculations are presented and compared with the accurate 3D calculations.
Liu, Tianhui; Zhang, Zhaojun; Fu, Bina; Yang, Xueming; Zhang, Dong H
2016-03-16
The mode-specific dynamics for the dissociative chemisorption of H2O on Cu(111) is first investigated by seven-dimensional quantum dynamics calculations, based on an accurately fitted potential energy surface (PES) recently developed by neural network fitting to DFT energy points. It is indicated that excitations in all three vibrational modes have a significant impact on reactivity, which are more efficacious than increasing the translational energy in promoting the reaction, with the largest enhancement for the excitation in the asymmetric stretching mode. There is large discrepancy between the six-dimensional reactivities with fixed azimuthal angles and seven-dimensional results, revealing that the 6D "flat surface" model cannot accurately characterize the reaction dynamics. The azimuthal angle-averaging approach is validated for vibrational excited states of the reactant, where the 7D mode-specific probability can be well reproduced by averaging the 6D azimuthal angle-fixed probabilities over 18 angles. PMID:26941197
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...
Hong, Mei; Mishanina, Tatiana V; Cady, Sarah D
2009-06-10
The use of side chain methyl (13)C chemical shifts for the determination of the rotameric conformation of Val and Leu residues in proteins by solid-state NMR spectroscopy is described. Examination of the solution NMR stereospecifically assigned methyl groups shows significant correlation between the difference in the two methyl carbons' chemical shifts and the side chain conformation. It is found that alpha-helical and beta-sheet backbones cause different side chain methyl chemical shift trends. In alpha-helical Leu's, a relatively large absolute methyl (13)C shift difference of 2.89 ppm is found for the most populated mt rotamer (chi(1) = -60 degrees, chi(2) = 180 degrees), while a much smaller value of 0.73 ppm is found for the next populated tp rotamer (chi(1) = 180 degrees, chi(2) = 60 degrees). For alpha-helical Val residues, the dominant t rotamer (chi(1) = 180 degrees) has more downfield Cgamma2 chemical shifts than Cgamma1 by 1.71 ppm, while the next populated m rotamer (chi(1) = -60 degrees) shows the opposite trend of more downfield Cgamma1 chemical shift by 1.23 ppm. These significantly different methyl (13)C chemical shifts exist despite the likelihood of partial rotameric averaging at ambient temperature. We show that these conformation-dependent methyl (13)C chemical shifts can be utilized for side chain structure determination once the methyl (13)C resonances are accurately measured by double-quantum (DQ) filtered 2D correlation experiments, most notably the dipolar DQ to single-quantum (SQ) correlation technique. The advantage of the DQ-SQ correlation experiment over simple 2D SQ-SQ correlation experiments is demonstrated on the transmembrane peptide of the influenza A M2 proton channel. The methyl chemical shifts led to predictions of the side chain rotameric states for several Val and Leu residues in this tetrameric helical bundle. The predicted Val rotamers were further verified by dipolar correlation experiments that directly measure the chi(1
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.
An efficient matrix product operator representation of the quantum chemical Hamiltonian
NASA Astrophysics Data System (ADS)
Keller, Sebastian; Dolfi, Michele; Troyer, Matthias; Reiher, Markus
2015-12-01
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.
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. PMID:17009357
Physico-chemical mechanism for the vapors sensitivity of photoluminescent InP quantum dots
NASA Astrophysics Data System (ADS)
Prosposito, P.; De Angelis, R.; De Matteis, F.; Hatami, F.; Masselink, W. T.; Zhang, H.; Casalboni, M.
2016-03-01
InP/InGaP surface quantum dots are interesting materials for optical chemical sensors since they present an intense emission at room temperature, whose intensity changes rapidly and reversibly depending on the composition of the environmental atmosphere. We present here their emission properties by time resolved photoluminescence spectroscopy investigation and we discuss the physico-chemical mechanism behind their sensitivity to the surrounding atmosphere. Photoluminescence transients in inert atmosphere (N2) and in solvent vapours of methanol, clorophorm, acetone and water were measured. The presence of vapors of clorophorm, acetone and water showed a very weak effect on the transient times, while an increase of up to 15% of the decay time was observed for methanol vapour exposure. On the basis of the vapor molecule nature (polarity, proticity, steric hindrance, etc.) and of the interaction of the vapor molecules with the quantum dots surface a sensing mechanism involving quantum dots non-radiative surface states is proposed.
An efficient matrix product operator representation of the quantum chemical Hamiltonian.
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. PMID:26723662
An efficient matrix product operator representation of the quantum chemical Hamiltonian
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.
Error Sensitivity to Environmental Noise in Quantum Circuits for Chemical State Preparation.
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
Recent Results in Quantum Chemical Kinetics from High Resolution Spectroscopy
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.
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.
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
Quantum Chemical Studies of Methane Monooxygenase: Comparison with P450
Guallar, Victor; Gherman, Benjamin F.; Lippard, Stephen J.; Friesner, Richard A.
2002-04-01
The catalytic pathways of soluble methane monooxygenase (sMMO) and cytochrome P450CAM, iron-containing enzymes, are described and compared. Recent extensive density functional ab initio electronic structure calculations have revealed many similarities in a number of the key catalytic steps, as well as some important differences. A particularly interesting and significant contrast is the role played by the protein in each system. For sMMO, the protein stabilizes various species in the catalytic cycle through a series of carboxylate shifts. This process is adequately described by a relatively compact model of the active site (similar to100 atoms), providing a reasonable description of the energetics of hydrogen atom abstraction. For P450CAM, in contrast, the inclusion of the full protein is necessary for an accurate description of the hydrogen atom abstraction.
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
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. PMID:26722872
NASA Astrophysics Data System (ADS)
Roy, Mathieu; Wilson, Brian C.
2008-02-01
We are investigating the use of ZnS-capped CdSe quantum dot (QD) bioconjugates combined with fluorescence endoscopy for improved early cancer detection in the esophagus, colon and lung. A major challenge in using fluorescent contrast agents in vivo is to extract the relevant signal from the tissue autofluorescence (AF). The present studies are aimed at maximizing the QD signal to AF background ratio (SBR) to facilitate detection. These contrast optimization studies require optical phantoms that simulate tissue autofluorescence, absorption and scattering over the entire visible spectrum, while allowing us to control the optical thickness. We present an optical phantom made of fresh homogenized tissue diluted in water. The homogenized tissue is poured into a clear polymer tank designed to hold a QD-loaded silica capillary in its center. Because of the non-linear effects of absorption and scattering on measured autofluorescence, direct comparison between results obtained using tissue phantoms of different concentration is not possible. We introduce mathematical models that make it possible to perform measurements on diluted tissue homogenates and subsequently extrapolate the results to intact (non-diluted) tissue. Finally, we present preliminary QD contrast data showing that the 380-420 nm spectral window is optimal for surface QD imaging.
Chemically Triggered Formation of Two-Dimensional Epitaxial Quantum Dot Superlattices.
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
Quantum chemical and spectroscopic investigations of 5-aminoquinoline.
Arjunan, V; Mohan, S; Balamourougane, P S; Ravindran, P
2009-12-01
The Fourier transform infrared (FTIR) and FT-Raman spectra of 5-aminoquinoline (5AQ) have been recorded in the range 4000-400 and 3500-100 cm(-1), respectively. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the observed FTIR and FT-Raman data. (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by using the gauge independent atomic orbital (GIAO) method. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The geometric parameters, chemical shifts and absorption wavelengths were compared with the experimental data of the molecule. The vibrational frequencies which were determined experimentally are compared with those obtained theoretically from ab initio HF and DFT-B3LYP gradient calculations employing the 6-31G** and 6-311++G** basis sets for optimized geometries of the compound. The interactions of NH-pi and the influence of amino group on the skeletal modes are investigated. PMID:19854675
Quantum chemical and spectroscopic investigations of 5-aminoquinoline
NASA Astrophysics Data System (ADS)
Arjunan, V.; Mohan, S.; Balamourougane, P. S.; Ravindran, P.
2009-12-01
The Fourier transform infrared (FTIR) and FT-Raman spectra of 5-aminoquinoline (5AQ) have been recorded in the range 4000-400 and 3500-100 cm -1, respectively. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the observed FTIR and FT-Raman data. 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by using the gauge independent atomic orbital (GIAO) method. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The geometric parameters, chemical shifts and absorption wavelengths were compared with the experimental data of the molecule. The vibrational frequencies which were determined experimentally are compared with those obtained theoretically from ab initio HF and DFT-B3LYP gradient calculations employing the 6-31G** and 6-311++G** basis sets for optimized geometries of the compound. The interactions of NH-π and the influence of amino group on the skeletal modes are investigated.
Felmy, Andrew R.; Mason, Marvin; Qafoku, Odeta; Xia, Yuanxian; Wang, Zheming; MacLean, Graham
2003-03-27
Developing accurate thermodynamic models for predicting the chemistry of the high-level waste tanks at Hanford is an extremely daunting challenge in electrolyte and radionuclide chemistry. These challenges stem from the extremely high ionic strength of the tank waste supernatants, presence of chelating agents in selected tanks, wide temperature range in processing conditions and the presence of important actinide species in multiple oxidation states. This presentation summarizes progress made to date in developing accurate models for these tank waste solutions, how these data are being used at Hanford and the important challenges that remain. New thermodynamic measurements on Sr and actinide complexation with specific chelating agents (EDTA, HEDTA and gluconate) will also be presented.
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.
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.
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. PMID:26851912
Quantum-Chemical Calculation of Carbododecahedron Formation in Carbon Plasma.
Poklonski, Nikolai A; Ratkevich, Sergey V; Vyrko, Sergey A
2015-08-27
The ground state of the molecule consisting of 10 carbon atoms in C10(rg) "ring" conformation and the energy of its metastable C10(st) "star" conformation are reported. The reaction coordinate for the isomeric transition C10(st) → C10(rg) was calculated using density functional theory (DFT) with UB3LYP/6-31G(d,p). It was established that a 5-fold symmetry axis is conserved in this isomeric transition. The total energy of the ring isomer is by 10.33 eV (9.16 eV as zero-point energy corrected) lower than that of the star isomer. The energy barrier for the transition from the metastable star state to the ring state is 2.87 eV (3.57 eV as zero-point energy corrected). An analysis of possible chemical reactions in carbon plasma involving C10(st) and C10(rg) and leading to the formation of C20 fullerenes was performed. It was revealed that the presence of the C10(st) conformation in the reaction medium is a necessary condition for C20 fullerene formation. It was shown that the presence of hydrogen atoms in carbon plasma and UV radiation accelerate the C10(st) → C10(rg) transition and thus suppress the C20 fullerene formation. PMID:26267290
Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence.
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. PMID:21344903
Brückner, Robin; Haller, Heike; Ellwanger, Mathias; Riedel, Sebastian
2012-04-27
Polychloride monoanions stabilized by quaternary ammonium salts are investigated using Raman spectroscopy and state-of-the-art quantum-chemical calculations. A regular V-shaped pentachloride is characterized for the [N(Me)(4)][Cl(5)] salt, whereas a hockey-stick-like structure is tentatively assigned for [N(Et)(4)][Cl(2)⋅⋅⋅Cl(3)(-)]. Increasing the size of the cation to the quaternary ammonium salts [NPr(4)](+) and [NBu(4)](+) leads to the formation of the [Cl(3)](-) anion. The latter is found to be a pale yellow liquid at about 40 °C, whereas all the other compounds exist as powders. Further to these observations, the novel [Cl(9)](-) anion is characterized by low-temperature Raman spectroscopy in conjunction with quantum-chemical calculations. PMID:22461376
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
Easton, Max E; Chan, Bun; Masters, Anthony F; Radom, Leo; Maschmeyer, Thomas
2016-03-01
The bonding environments of some polybromide monoanions and networks were examined by quantum-chemical methods to investigate electronic interactions between dibromine-dibromine contacts. Examination of thermodynamic parameters and a bond critical point analysis give strong evidence for such bonding modes, which have been previously treated disparately in the literature. The thermodynamic stability of large polybromides up to [Br37 ](-) was also predicted by these methods. PMID:26833846
Elucidating the interaction of H2O2 with polar amino acids - Quantum chemical calculations
NASA Astrophysics Data System (ADS)
Karmakar, Tarak; Balasubramanian, Sundaram
2014-10-01
Quantum chemical calculations have been carried out to investigate the interaction motifs of H2O2 with polar amino acid residues. Binding energies obtained from gas phase and continuum solvent phase calculations range between 2 and 30 kcal/mol. H2O2 interacts with the side chain of polar amino acids chiefly through the formation of hydrogen bonds. The sbnd CH group in side chains of a few residues provides additional stabilization to H2O2.
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.
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.
Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy
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
Vila, Jorge A.; Aramini, James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Tong, Liang; Montelione, Gaetano T.; Scheraga, Harold A.
2008-01-01
A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures. PMID:18787110
Pandey, Manoj Kumar; Ramamoorthy, Ayyalusamy
2013-01-01
There is considerable interest in determining amide-15N chemical shift anisotropy (CSA) tensors from biomolecules and understanding their variation for structural and dynamics studies using solution and solid-state NMR spectroscopy and also by quantum chemical calculations. Due to the difficulties associated with the measurement of CSA tensors from membrane proteins, NMR-based structural studies heavily relied on the CSA tensors determined from model systems, typically single crystals of model peptides. In the present study, the principal components of backbone amide-15N CSA tensor have been determined using density functional theory for a 16.7-kDa membrane-bound paramagnetic heme containing protein, cytochrome b5 (cytb5). All the calculations were performed by taking residues within 5Å distance from the backbone amide-15N nucleus of interest. The calculated amide-15N CSA spans agree less well with our solution NMR data determined for an effective internuclear distance rN-H = 1.023 Å and a constant angle β = 18° that the least shielded component (δ11) makes with the N-H bond. The variation of amide-15N CSA span obtained using quantum chemical calculations is found to be smaller than that obtained from solution NMR measurements, whereas the trends of the variations are found to be in close agreement. We believe that the results reported in this study will be useful in studying the structure and dynamics of membrane proteins and heme-containing proteins, and also membrane-bound protein-protein complexes such as cytochromes-b5-P450. PMID:23268659
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.
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.
On the Chemical Basis of Trotter-Suzuki Errors in Quantum Chemistry Simulation
NASA Astrophysics Data System (ADS)
Babbush, Ryan; McClean, Jarrod; Wecker, Dave; Aspuru-Guzik, Alán; Wiebe, Nathan
2015-03-01
Although the simulation of quantum chemistry is one of the most anticipated applications of quantum computing, the scaling of known upper bounds on the complexity of these algorithms is daunting. Prior work has bounded errors due to Trotterization in terms of the norm of the error operator and analyzed scaling with respect to the number of spin-orbitals. However, we find that these error bounds can be loose by up to sixteen orders of magnitude for some molecules. Furthermore, numerical results for small systems fail to reveal any clear correlation between ground state error and number of spin-orbitals. We instead argue that chemical properties, such as the maximum nuclear charge in a molecule and the filling fraction of orbitals, can be decisive for determining the cost of a quantum simulation. Our analysis motivates several strategies to use classical processing to further reduce the required Trotter step size and to estimate the necessary number of steps, without requiring additional quantum resources. Finally, we demonstrate improved methods for state preparation techniques which are asymptotically superior to proposals in the simulation literature.
Chemical basis of Trotter-Suzuki errors in quantum chemistry simulation
NASA Astrophysics Data System (ADS)
Babbush, Ryan; McClean, Jarrod; Wecker, Dave; Aspuru-Guzik, Alán; Wiebe, Nathan
2015-02-01
Although the simulation of quantum chemistry is one of the most anticipated applications of quantum computing, the scaling of known upper bounds on the complexity of these algorithms is daunting. Prior work has bounded errors due to discretization of the time evolution (known as "Trotterization") in terms of the norm of the error operator and analyzed scaling with respect to the number of spin orbitals. However, we find that these error bounds can be loose by up to 16 orders of magnitude for some molecules. Furthermore, numerical results for small systems fail to reveal any clear correlation between ground-state error and number of spin orbitals. We instead argue that chemical properties, such as the maximum nuclear charge in a molecule and the filling fraction of orbitals, can be decisive for determining the cost of a quantum simulation. Our analysis motivates several strategies to use classical processing to further reduce the required Trotter step size and estimate the necessary number of steps, without requiring additional quantum resources. Finally, we demonstrate improved methods for state preparation techniques which are asymptotically superior to proposals in the simulation literature.
The Radical Pair Mechanism and the Avian Chemical Compass: Quantum Coherence and Entanglement
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.
Grid-based methods for biochemical ab initio quantum chemical applications
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.
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.
2015-01-01
Performance characteristics of gas-phase microsensors will determine the ultimate utility of these devices for a wide range of chemical monitoring applications. Commonly employed chemiresistor elements are quite sensitive to selected analytes, and relatively new methods have increased the selectivity to specific compounds, even in the presence of interfering species. Here, we have focused on determining whether purposefully driven temperature modulation can produce faster sensor-response characteristics, which could enable measurements for a broader range of applications involving dynamic compositional analysis. We investigated the response speed of a single chemiresitive In2O3 microhotplate sensor to four analytes (methanol, ethanol, acetone, 2-butanone) by systematically varying the oscillating frequency (semicycle periods of 20–120 ms) of a bilevel temperature cycle applied to the sensing element. It was determined that the fastest response (≈ 9 s), as indicated by a 98% signal-change metric, occurred for a period of 30 ms and that responses under such modulation were dramatically faster than for isothermal operation of the same device (>300 s). Rapid modulation between 150 and 450 °C exerts kinetic control over transient processes, including adsorption, desorption, diffusion, and reaction phenomena, which are important for charge transfer occurring in transduction processes and the observed response times. We also demonstrate that the fastest operation is accompanied by excellent discrimination within a challenging 16-category recognition problem (consisting of the four analytes at four separate concentrations). This critical finding demonstrates that both speed and high discriminatory capabilities can be realized through temperature modulation. PMID:24931319
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.
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
Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon
2015-01-01
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 77Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state 77Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information of selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on 77Se 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. 77Se 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
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.
Biomimetic, Mild Chemical Synthesis of CdTe-GSH Quantum Dots with Improved Biocompatibility
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
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…
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.
Quantum chemical modelling of ``green'' luminescence in ABO
NASA Astrophysics Data System (ADS)
Eglitis, R. I.; Kotomin, E. A.; Borstel, G.
2002-06-01
The origin of the intrinsic excitonic (``green'') luminescence in ABO3 perovskites remains a hot topic over the last quarter of a century. We suggest as a theoretical interpretation for the ``green'' luminescence in these crystals, the recombination of electron and hole polarons forming a charge transfer vibronic exciton. In order to check quantitatively the proposed model, we performed quantum chemical calculations using the Intermediate Neglect of Differential Overlap (INDO) method combined with the periodic defect model. The luminescence energies calculated for four perovskite crystals are found to be in good agreement with experimental data.
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. PMID:25947046
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.
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.
The molecular structure of barium dibromide: an electron diffraction and quantum chemical study
NASA Astrophysics Data System (ADS)
Hargittai, Magdolna; Kolonits, Mária; Schultz, György
2001-06-01
The molecular structure of barium dibromide was determined by gas-phase electron diffraction, ab initio quantum chemical calculations, and joint electron diffraction/vibratonal spectroscopic analyses. All techniques yield consistently an unambiguously bent geometry. The following geometrical parameters were obtained: rg(Ba-Br) 2.911±0.006 Å, re(Ba-Br) 2.899±0.007 Å, ∠ aBr-Ba-Br 137.0±2.5° and ∠ eBr-Ba-Br 137.1±4.9°.
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
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.
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.
Patil, Vaishali M; Das, Sukanya; Balasubramanian, Krishnan
2016-05-26
We combine quantum chemical and molecular docking techniques to provide new insights into how piperine molecule in various forms of pepper enhances bioavailability of a number of drugs including curcumin in turmeric for which it increases its bioavailability by a 20-fold. We have carried out docking studies of quantum chemically optimized piperine structure binding to curcumin, CYP3A4 in cytochrome P450, p-Glycoprotein and UDP-glucuronosyltransferase (UGT), the enzyme responsible for glucuronosylation, which increases the solubility of curcumin. All of these studies establish that piperine binds to multiple sites on the enzymes and also intercalates with curcumin forming a hydrogen bonded complex with curcumin. The conjugated network of double bonds and the presence of multiple charge centers of piperine offer optimal binding sites for piperine to bind to enzymes such as UDP-GDH, UGT, and CYP3A4. Piperine competes for curcumin's intermolecular hydrogen bonding and its stacking propensity by hydrogen bonding with enolic proton of curcumin. This facilitates its metabolic transport, thereby increasing its bioavailability both through intercalation into curcumin layers through intermolecular hydrogen bonding, and by inhibiting enzymes that cause glucuronosylation of curcumin. PMID:27111639
Coherent chemical kinetics as quantum walks. I. Reaction operators for radical pairs
NASA Astrophysics Data System (ADS)
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), 10.1063/1.4844355], in contrast to previous work by Jones and Hore [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010), 10.1016/j.cplett.2010.01.063]. 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.
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.
Computer simulations of local anesthetic mechanisms: Quantum chemical investigation of procaine
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.
Efficient Implementation of Many-body Quantum Chemical Methods on the Intel Xeon Phi Coprocessor
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.
Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors.
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. PMID:27347738
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. PMID:27277206
NASA Astrophysics Data System (ADS)
Xu, Zhongnan; Joshi, Yogesh V.; Raman, Sumathy; Kitchin, John R.
2015-04-01
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.
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.
A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules
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.
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.
NASA Astrophysics Data System (ADS)
Nadarajah, A.; Smith, T.; Könenkamp, R.
2012-12-01
We report a nanowire-quantum-dot-polymer solar cell consisting of a chemically treated CdSe quantum dot film deposited on n-type ZnO nanowires. The electron and hole collecting contacts are a fluorine-doped tin-oxide/zinc oxide layer and a P3HT/Au layer. This device architecture allows for enhanced light absorption and an efficient collection of photogenerated carriers. A detailed analysis of the chemical treatment of the quantum dots, their deposition, and the necessary annealing processes are discussed. We find that the surface treatment of CdSe quantum dots with pyridine, and the use of 1,2-ethanedithiol (EDT) ligands, critically improves the device performance. Annealing at 380 °C for 2 h is found to cause a structural conversion of the CdSe from its initial isolated quantum dot arrangement into a polycrystalline film with excellent surface conformality, thereby resulting in a further enhancement of device performance. Moreover, long-term annealing of 24 h leads to additional increases in device efficiency. Our best conversion efficiency reached for this type of cell is 3.4% under 85 mW cm-2 illumination.
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.
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
Quantum Dot and Polymer Composite Cross-Reactive Array for Chemical Vapor Detection.
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
Arjunan, V; Thillai Govindaraja, S; Jose, Sujin P; Mohan, S
2014-07-15
The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm(-1) respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G(**), high level 6-311++G(**) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The (1)H (400 MHz; CDCl3) and (13)C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors. PMID:24662754
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.
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.
Quantum Chemical Analysis of MHC-Peptide Interactions for Vaccine Design
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
A quantum chemical perspective on (6-4) photolesion repair by photolyases.
Dreuw, Andreas; Faraji, Shirin
2013-12-14
(6-4)-Photolyases are fascinating enzymes which repair (6-4)-DNA photolesions utilizing light themselves. It is well known that upon initial photo-excitation of an antenna pigment an electron is transferred from an adjacent FADH(-) cofactor to the photolesion initiating repair, i.e. restoration of the original undamaged DNA bases. Concerning the molecular details of this amazing repair mechanism, the early steps of energy transfer and catalytic electron generation are well understood, the terminal repair mechanism, however, is still a matter of ongoing debate. In this perspective article, recent results of quantum chemical investigations are presented, and their meaning for the repair mechanism under natural conditions is outlined. Consequences of natural light conditions, temperature and thermal equilibration are highlighted when issues like the initial protonation state of the relevant histidines and the lesion, or the direction of electron transfer are discussed. PMID:24145385
Quantum-chemical and picosecond investigations of excited states of thioindigoid dyes
Fabian, Yu.; Krysanov, S.A.; Alfimov, M.V.
1987-11-01
The thioindigoid dyes are convenient objects for studying reverse trans-cis photoisomerization. This is due to the extensive use of nanosecond photolysis. In this work, in order to interpret some new absorption bands, the authors compare the results of quantum-chemical and picosecond investigations of solutions of the trans isomers of thioindigo and a perinaphthothioindigoid dye. A double-beam optical system, which makes it possible to record the kinetics of the variation of the induced absorption in the range from several picoseconds to 5 nsec, was used for the real-time scanning of the continuum instead of an echelon. The spectroscopic properties of the thioindigoid chromophore can be understood in the framework of standard calculations by the Pariser-Parr-Pople method.
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.
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.
Quantum chemical investigations on the nonradiative deactivation pathways of cytosine derivatives.
Nakayama, Akira; Yamazaki, Shohei; Taketsugu, Tetsuya
2014-10-01
The nonradiative deactivation pathways of cytosine derivatives (cytosine, 5-fluorocytosine, 5-methylcytosine, and 1-methycytosine) and their tautomers are investigated by quantum chemical calculations, and the substituent effects on the deactivation process are examined. The MS-CASPT2 method is employed in the excited-state geometry optimization and also in the search for conical intersection points, and the potential energy profiles connecting the Franck-Condon point, excited-state minimum energy structures, and the conical intersection points are investigated. Our calculated vertical and adiabatic excitation energies are in quite good agreement with the experimental results, and the relative barrier heights leading to the conical intersections are correlated with the experimentally observed excite-state lifetimes, where the calculated barrier heights are in the order of cytosine < 5-methylcytosine < 5-fluorocytosine. PMID:25178384
Van Regemorter, T; Guillaume, M; Fuchs, A; Lennartz, C; Geskin, V; Beljonne, D; Cornil, J
2012-11-01
The formation of dipoles at interfaces between organic semiconductors is expected to play a significant role in the operation of organic-based devices, though the electronic processes at their origin have still to be clearly elucidated. Quantum-chemical calculations can prove very useful to shed light on such electronic interfacial phenomena provided that a suitable theoretical approach is used. In this context, we have performed calculations on small vertical stacks of TTF-TCNQ molecules, first at the CAS-MRCI level to validate the use of single-determinantal approaches, then at the MP2 level set as a benchmark. Various density functional theory (DFT) functionals have then been applied to larger stacks, showing that long-range corrected functionals are required to reproduce MP2 results taken as benchmark. Finally, the use of periodic boundary conditions at the DFT level points to the huge impact of depolarization effects between adjacent stacks. PMID:23145743
NASA Astrophysics Data System (ADS)
Van Regemorter, T.; Guillaume, M.; Fuchs, A.; Lennartz, C.; Geskin, V.; Beljonne, D.; Cornil, J.
2012-11-01
The formation of dipoles at interfaces between organic semiconductors is expected to play a significant role in the operation of organic-based devices, though the electronic processes at their origin have still to be clearly elucidated. Quantum-chemical calculations can prove very useful to shed light on such electronic interfacial phenomena provided that a suitable theoretical approach is used. In this context, we have performed calculations on small vertical stacks of TTF-TCNQ molecules, first at the CAS-MRCI level to validate the use of single-determinantal approaches, then at the MP2 level set as a benchmark. Various density functional theory (DFT) functionals have then been applied to larger stacks, showing that long-range corrected functionals are required to reproduce MP2 results taken as benchmark. Finally, the use of periodic boundary conditions at the DFT level points to the huge impact of depolarization effects between adjacent stacks.
Prism-C2n carbon dimer, trimer, and nano-sheets: A quantum chemical study
NASA Astrophysics Data System (ADS)
Ohno, Koichi; Satoh, Hiroko; Iwamoto, Takeaki
2015-07-01
Quantum chemical calculations have predicted the existence of a new carbon family with double-layered structures formed by arranging prism-C2n (n = 6, 8, and 12) units. Theoretical explorations of potential energy surfaces suggest the lowest barriers of the reaction channels to be ca. 30 kJ mol-1 for a D2h prism-C16 dimer and a D3h prism-C24 trimer. Geometry optimizations under periodic boundary conditions yield some prism-C2n sheets composed of CC single bonds of ca. 0.15-0.16 nm. The relative energies per one atom with respect to graphene are 90-160 kJ mol-1. Van der Waals thickness is estimated to be ca. 0.5 nm.
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.
III-nitride quantum cascade detector grown by metal organic chemical vapor deposition
Song, Yu Huang, Tzu-Yung; Badami, Pranav; Gmachl, Claire; Bhat, Rajaram; Zah, Chung-En
2014-11-03
Quantum cascade (QC) detectors in the GaN/Al{sub x}Ga{sub 1−x}N material system grown by metal organic chemical vapor deposition are designed, fabricated, and characterized. Only two material compositions, i.e., GaN as wells and Al{sub 0.5}Ga{sub 0.5}N as barriers are used in the active layers. The QC detectors operates around 4 μm, with a peak responsivity of up to ∼100 μA/W and a detectivity of up to 10{sup 8} Jones at the background limited infrared performance temperature around 140 K.
Property and quantum chemical investigation of poly(ethyl α-cyanoacrylate)
NASA Astrophysics Data System (ADS)
Zhou, Yahong; Bei, Fengli; Ji, Haiyan; Yang, Xujie; Lu, Lude; Wang, Xin
2005-03-01
The poly(ethyl α-cyanoacrylate) (PEtCNA) was synthesized by anionic polymerization. With the composed PEtCNA, its IR spectrum, 1HNMR spectrum and configuration are measured. Meanwhile, molecular geometry, electronic structure, IR spectrum and thermodynamic property of reactant and transition state on the reaction potential energy level of ethyl α-cyanoacrylate with hydroxyl have been completely optimized and calculated for the first time by the density functional theory DFT-B3LYP method and on the level of 6-31+G* group. The order of 10 10 s -1 of initiating rate constant in gas phase was obtained for the reaction. These were reported the quantum chemical calculation results so as to deepen researches on the relationship between structure and properties.
Unpolarized and polarized Raman spectroscopy of nylon-6 polymorphs: a quantum chemical approach.
Milani, Alberto
2015-03-01
Exploiting the very recent potentialities of state-of-the-art quantum chemical simulations of crystalline solids, unpolarized Raman spectra of α and γ polymorphs of Nylon-6 obtained through periodic density functional theory calculations are presented for the first time. The computed spectra are compared with the experimental spectra reported in the literature and allow a detailed interpretation to be proposed of the patterns observed, identifying unambiguous Raman marker bands of the different phases. The calculations of single crystal directional intensities gave the further possibility to predict the polarization properties of the Raman spectra of these polymorphs: considering in particular the α phase, polarized Raman spectra have been computed and showed a very good agreement with measurements previously reported for uniaxially oriented samples. PMID:25686634
Low temperature regulated growth of PbS quantum dots by wet chemical method
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.
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.
Quantum chemical studies of the pyrrole-water and pyridine-water complexes
NASA Astrophysics Data System (ADS)
Martoprawiro, Muhamad A.; Bacskay, George B.
An ab initio quantum chemical study of the hydrogen bonded binary complexes pyrrole-water and pyridine-water is reported. The calculations were performed largely at the MP2 level of theory using basis sets of double-zeta-plus polarization functions quality and focus on properties of the complexes such as molecular geometries, energies, harmonic vibrational frequencies, dipole moments and 14N nuclear quadrupole coupling constants. Where possible, the results of the calculations are compared with experimental data. In addition, the interaction potentials are studied in some detail, specifically with regard to basis set superposition and its effect on geometries, intermolecular vibrational frequencies and binding energies. The nature of interaction, i.e., the importance of electrostatic, Pauli repulsion, polarization, charge transfer and dispersion contributions to the hydrogen bond energies, as obtained in constrained spatial orbital variation analyses, is also discussed.
On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study
NASA Astrophysics Data System (ADS)
Durbeej, Bo; Eriksson, Leif A.
2003-06-01
The structural origin of the bathochromic shift assumed by the electronic absorption spectrum of protein-bound astaxanthin, the carotenoid that upon binding to crustacyanin is responsible for the blue colouration of lobster shell, is investigated by means of quantum chemical methods. The calculations suggest that the bathochromic shift is largely due to one of the astaxanthin C4 keto groups being hydrogen-bonded to a histidine residue of the surrounding protein, and that the effect of this histidine is directly dependent on its protonation state. Out of the different methodologies (CIS, TD-DFT, and ZINDO/S) employed to calculate wavelengths of maximum absorption, the best agreement with experimental data is obtained using the semiempirical ZINDO/S method.
A combined experimental and theoretical quantum chemical studies on 4-morpholinecarboxaldehyde
NASA Astrophysics Data System (ADS)
Arjunan, V.; Rani, T.; Santhanalakshmi, K.; Mohan, S.
2011-09-01
Extensive spectroscopic investigations have been carried out by recording the Fourier transform infrared (FTIR) and FT-Raman spectra and carrying out the theoretical quantum chemical studies on 4-morpholinecarboxaldehyde (4MC). From the ab initio and DFT analysis using HF, B3LYP and B3PW91 methods with 6-31G(d,p) and 6-311G++(d,p) basis sets the energies, structural, thermodynamical and vibrational characteristics of the compound were determined. The energy difference between the chair equatorial and chair axial conformers of 4MC have been calculated by density functional theory (DFT) method. The optimised geometrical parameters, theoretical wavenumbers and thermodynamic properties of the molecule were compared with the experimental values. The effect of carbonyl group on the characteristic frequencies of the morpholine ring has been analysed. The mixing of the fundamental modes with the help of potential energy distribution (PED) through normal co-ordinate analysis has been discussed.
NMR Hyperfine Shifts in Blue Copper Proteins: A Quantum Chemical Investigation
Zhang, Yong; Oldfield, Eric
2009-01-01
We present the results of the first quantum chemical investigations of 1H NMR hyperfine shifts in the blue copper proteins (BCPs): amicyanin, azurin, pseudoazurin, plastocyanin, stellacyanin, and rusticyanin. We find that very large structural models that incorporate extensive hydrogen bond networks, as well as geometry optimization, are required to reproduce the experimental NMR hyperfine shift results, the best theory vs experiment predictions having R2 = 0.94, a slope = 1.01, and a SD = 40.5 ppm (or ~4.7% of the overall ~860 ppm shift range). We also find interesting correlations between the hyperfine shifts and the bond and ring critical point properties computed using atoms-in-molecules theory, in addition to finding that hyperfine shifts can be well-predicted by using an empirical model, based on the geometry-optimized structures, which in the future should be of use in structure refinement. PMID:18314973