Electron-beam generated porous dextran gels: experimental and quantum chemical studies.

PubMed

Naumov, Sergej; Knolle, Wolfgang; Becher, Jana; Schnabelrauch, Matthias; Reichelt, Senta

2014-06-01

The aim of this work was to investigate the reaction mechanism of electron-beam generated macroporous dextran cryogels by quantum chemical calculation and electron paramagnetic resonance measurements. Electron-beam radiation was used to initiate the cross-linking reaction of methacrylated dextran in semifrozen aqueous solutions. The pore morphology of the resulting cryogels was visualized by scanning electron microscopy. Quantum chemical calculations and electron paramagnetic resonance studies provided information on the most probable reaction pathway and the chain growth radicals. The most probable reaction pathway was a ring opening reaction and the addition of a C-atom to the double-bond of the methacrylated dextran molecule. First detailed quantum chemical calculation on the reaction mechanism of electron-beam initiated cross-linking reaction of methacrylated dextran are presented.

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

PubMed

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

Ground state energy of solid molecular hydrogen at high pressure

NASA Technical Reports Server (NTRS)

Ebner, C.; Sung, C. C.

1972-01-01

The present status of the theoretical equation of state of solid molecular hydrogen is reviewed. Different quantum mechanical calculations by several groups lead to results which generally agree with each other but which disagree systematically with the measured pressure-volume curve at pressures larger than about 3000 atm. A new calculation of this curve is presented including the effect of the anisotropic interaction between H2 molecules within a completely quantum-mechanical formalism. The results show that inclusion of this interaction removes the discrepancy between theory and experiment at high pressures and that a quantum-mechanical treatment is necessary to realize its full effect.

Holographic description of a quantum black hole on a computer

NASA Astrophysics Data System (ADS)

Hanada, Masanori; Hyakutake, Yoshifumi; Ishiki, Goro; Nishimura, Jun

2014-05-01

Black holes have been predicted to radiate particles and eventually evaporate, which has led to the information loss paradox and implies that the fundamental laws of quantum mechanics may be violated. Superstring theory, a consistent theory of quantum gravity, provides a possible solution to the paradox if evaporating black holes can actually be described in terms of standard quantum mechanical systems, as conjectured from the theory. Here, we test this conjecture by calculating the mass of a black hole in the corresponding quantum mechanical system numerically. Our results agree well with the prediction from gravity theory, including the leading quantum gravity correction. Our ability to simulate black holes offers the potential to further explore the yet mysterious nature of quantum gravity through well-established quantum mechanics.

'Quantum interference with slits' revisited

NASA Astrophysics Data System (ADS)

Rothman, Tony; Boughn, Stephen

2011-01-01

Marcella has presented a straightforward technique employing the Dirac formalism to calculate single- and double-slit interference patterns. He claims that no reference is made to classical optics or scattering theory and that his method therefore provides a purely quantum mechanical description of these experiments. He also presents his calculation as if no approximations are employed. We show that he implicitly makes the same approximations found in classical treatments of interference and that no new physics has been introduced. At the same time, some of the quantum mechanical arguments Marcella gives are, at best, misleading.

Relativistic quantum mechanical calculations of electron-impact broadening for spectral lines in Be-like ions

NASA Astrophysics Data System (ADS)

Duan, B.; Bari, M. A.; Wu, Z. Q.; Jun, Y.; Li, Y. M.; Wang, J. G.

2012-11-01

Aims: We present relativistic quantum mechanical calculations of electron-impact broadening of the singlet and triplet transition 2s3s ← 2s3p in four Be-like ions from N IV to Ne VII. Methods: In our theoretical calculations, the K-matrix and related symmetry information determined by the colliding systems are generated by the DARC codes. Results: A careful comparison between our calculations and experimental results shows good agreement. Our calculated widths of spectral lines also agree with earlier theoretical results. Our investigations provide new methods of calculating electron-impact broadening parameters for plasma diagnostics.

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

PubMed

Ferenczy, György G

2013-04-05

The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem. Copyright © 2013 Wiley Periodicals, Inc.

Canonical partition functions: ideal quantum gases, interacting classical gases, and interacting quantum gases

NASA Astrophysics Data System (ADS)

Zhou, Chi-Chun; Dai, Wu-Sheng

2018-02-01

In statistical mechanics, for a system with a fixed number of particles, e.g. a finite-size system, strictly speaking, the thermodynamic quantity needs to be calculated in the canonical ensemble. Nevertheless, the calculation of the canonical partition function is difficult. In this paper, based on the mathematical theory of the symmetric function, we suggest a method for the calculation of the canonical partition function of ideal quantum gases, including ideal Bose, Fermi, and Gentile gases. Moreover, we express the canonical partition functions of interacting classical and quantum gases given by the classical and quantum cluster expansion methods in terms of the Bell polynomial in mathematics. The virial coefficients of ideal Bose, Fermi, and Gentile gases are calculated from the exact canonical partition function. The virial coefficients of interacting classical and quantum gases are calculated from the canonical partition function by using the expansion of the Bell polynomial, rather than calculated from the grand canonical potential.

Holographic description of a quantum black hole on a computer.

PubMed

Hanada, Masanori; Hyakutake, Yoshifumi; Ishiki, Goro; Nishimura, Jun

2014-05-23

Black holes have been predicted to radiate particles and eventually evaporate, which has led to the information loss paradox and implies that the fundamental laws of quantum mechanics may be violated. Superstring theory, a consistent theory of quantum gravity, provides a possible solution to the paradox if evaporating black holes can actually be described in terms of standard quantum mechanical systems, as conjectured from the theory. Here, we test this conjecture by calculating the mass of a black hole in the corresponding quantum mechanical system numerically. Our results agree well with the prediction from gravity theory, including the leading quantum gravity correction. Our ability to simulate black holes offers the potential to further explore the yet mysterious nature of quantum gravity through well-established quantum mechanics. Copyright © 2014, American Association for the Advancement of Science.

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

PubMed

Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; Luo, Ray; Lee, Taisung; Caldwell, James; Wang, Junmei; Kollman, Peter

2003-12-01

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999-2012, 2003

Quantum versus classical dynamics in the optical centrifuge

NASA Astrophysics Data System (ADS)

Armon, Tsafrir; Friedland, Lazar

2017-09-01

The interplay between classical and quantum-mechanical evolution in the optical centrifuge (OC) is discussed. The analysis is based on the quantum-mechanical formalism starting from either the ground state or a thermal ensemble. Two resonant mechanisms are identified, i.e., the classical autoresonance and the quantum-mechanical ladder climbing, yielding different dynamics and rotational excitation efficiencies. The rotating-wave approximation is used to analyze the two resonant regimes in the associated dimensionless two-parameter space and calculate the OC excitation efficiency. The results show good agreement between numerical simulations and theory and are relevant to existing experimental setups.

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

PubMed

Muddana, Hari S; Gilson, Michael K

2012-06-12

The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

PubMed

Mörschel, Philipp; Schmidt, Martin U

2015-01-01

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine

NASA Astrophysics Data System (ADS)

Cautereels, Julie; Blockhuys, Frank

2017-06-01

The quantum chemical mass spectrometry for materials science (QCMS2) method is used to verify the proposed mechanism for proton transfer - the Mobile Proton Model (MPM) - by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS2 framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of five-membered ring intermediates to include larger-ring intermediates. [Figure not available: see fulltext.

Vibrational analysis and quantum chemical calculations of 2,2‧-bipyridine Zinc(II) halide complexes

NASA Astrophysics Data System (ADS)

Ozel, Aysen E.; Kecel, Serda; Akyuz, Sevim

2007-05-01

In this study the molecular structure and vibrational spectra of Zn(2,2'-bipyridine)X 2 (X = Cl and Br) complexes were studied in their ground states by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimization, vibrational wavenumber and intensity calculations of free and coordinated 2,2'-bipyridine were carried out with the Gaussian03 program package by using Hartree-Fock (HF) and Density Functional Theory (DFT) with B3LYP functional and 6-31G (d,p) basis set. The total energy distributions (TED) of the vibrational modes were calculated by using Scaled Quantum Mechanical (SQM) analysis. Fundamentals were characterised by their total energy distributions. Coordination sensitive modes of 2,2'-bipyridine were determined.

Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory

NASA Technical Reports Server (NTRS)

Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.

1990-01-01

New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.

The Variation Theorem Applied to H-2+: A Simple Quantum Chemistry Computer Project

ERIC Educational Resources Information Center

Robiette, Alan G.

1975-01-01

Describes a student project which requires limited knowledge of Fortran and only minimal computing resources. The results illustrate such important principles of quantum mechanics as the variation theorem and the virial theorem. Presents sample calculations and the subprogram for energy calculations. (GS)

Predicted phototoxicities of carbon nano-material by quantum mechanical calculations.

EPA Science Inventory

The basis of this research is obtaining the best quantum mechanical structure of carbon nanomaterials and is fundamental in determining their other properties. Therefore, their predictive phototoxicity is directly related to the materials’ structure. The results of this project w...

Wave-Mechanical Properties of Stationary States.

ERIC Educational Resources Information Center

Holden, Alan

This monograph is a review of the quantum mechanical concepts presented in two other monographs, "The Nature of Atoms" and "Bonds Between Atoms," by the same author. It is assumed the reader is familiar with these ideas. The monograph sketches only those aspects of quantum mechanics that are of most direct use in picturing and calculating the…

Estimation of the Young’s modulus of cellulose Iß by MM3 and quantum mechanics

USDA-ARS?s Scientific Manuscript database

Young’s modulus provides a measure of the resistance to deformation of an elastic material. In this study, modulus estimations for models of cellulose Iß relied on calculations performed with molecular mechanics (MM) and quantum mechanics (QM) programs. MM computations used the second generation emp...

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

Some foundational aspects of quantum computers and quantum robots.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benioff, P.; Physics

1998-01-01

This paper addresses foundational issues related to quantum computing. The need for a universally valid theory such as quantum mechanics to describe to some extent its own validation is noted. This includes quantum mechanical descriptions of systems that do theoretical calculations (i.e. quantum computers) and systems that perform experiments. Quantum robots interacting with an environment are a small first step in this direction. Quantum robots are described here as mobile quantum systems with on-board quantum computers that interact with environments. Included are discussions on the carrying out of tasks and the division of tasks into computation and action phases. Specificmore » models based on quantum Turing machines are described. Differences and similarities between quantum robots plus environments and quantum computers are discussed.« less

Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer.

PubMed

Świderek, Katarzyna; Arafet, Kemel; Kohen, Amnon; Moliner, Vicent

2017-03-14

Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid quantum mechanics/molecular mechanics (QM/MM) potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE). Dynamics and quantum-tunneling effects are revealed to have little effect on the reaction rate, but are significant in determining the KIEs and their temperature dependence. A good agreement with experiments is found, especially when computed for RM1/MM simulations. The small temperature dependence of quantum tunneling corrections and the quasiclassical contribution term cancel each other, while the recrossing transmission coefficient seems to be temperature-independent over the interval of 5-40 °C.

Does ℏ play a role in multidimensional spectroscopy? Reduced hierarchy equations of motion approach to molecular vibrations.

PubMed

Sakurai, Atsunori; Tanimura, Yoshitaka

2011-04-28

To investigate the role of quantum effects in vibrational spectroscopies, we have carried out numerically exact calculations of linear and nonlinear response functions for an anharmonic potential system nonlinearly coupled to a harmonic oscillator bath. Although one cannot carry out the quantum calculations of the response functions with full molecular dynamics (MD) simulations for a realistic system which consists of many molecules, it is possible to grasp the essence of the quantum effects on the vibrational spectra by employing a model Hamiltonian that describes an intra- or intermolecular vibrational motion in a condensed phase. The present model fully includes vibrational relaxation, while the stochastic model often used to simulate infrared spectra does not. We have employed the reduced quantum hierarchy equations of motion approach in the Wigner space representation to deal with nonperturbative, non-Markovian, and nonsecular system-bath interactions. Taking the classical limit of the hierarchy equations of motion, we have obtained the classical equations of motion that describe the classical dynamics under the same physical conditions as in the quantum case. By comparing the classical and quantum mechanically calculated linear and multidimensional spectra, we found that the profiles of spectra for a fast modulation case were similar, but different for a slow modulation case. In both the classical and quantum cases, we identified the resonant oscillation peak in the spectra, but the quantum peak shifted to the red compared with the classical one if the potential is anharmonic. The prominent quantum effect is the 1-2 transition peak, which appears only in the quantum mechanically calculated spectra as a result of anharmonicity in the potential or nonlinearity of the system-bath coupling. While the contribution of the 1-2 transition is negligible in the fast modulation case, it becomes important in the slow modulation case as long as the amplitude of the frequency fluctuation is small. Thus, we observed a distinct difference between the classical and quantum mechanically calculated multidimensional spectra in the slow modulation case where spectral diffusion plays a role. This fact indicates that one may not reproduce the experimentally obtained multidimensional spectrum for high-frequency vibrational modes based on classical molecular dynamics simulations if the modulation that arises from surrounding molecules is weak and slow. A practical way to overcome the difference between the classical and quantum simulations was discussed.

Algorithm for quantum-mechanical finite-nuclear-mass variational calculations of atoms with two p electrons using all-electron explicitly correlated Gaussian basis functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharkey, Keeper L.; Pavanello, Michele; Bubin, Sergiy

2009-12-15

A new algorithm for calculating the Hamiltonian matrix elements with all-electron explicitly correlated Gaussian functions for quantum-mechanical calculations of atoms with two p electrons or a single d electron have been derived and implemented. The Hamiltonian used in the approach was obtained by rigorously separating the center-of-mass motion and it explicitly depends on the finite mass of the nucleus. The approach was employed to perform test calculations on the isotopes of the carbon atom in their ground electronic states and to determine the finite-nuclear-mass corrections for these states.

Stark broadening of the B III 2s-2p lines

NASA Astrophysics Data System (ADS)

Griem, Hans R.; Ralchenko, Yuri V.; Bray, Igor

1997-12-01

We present a quantum-mechanical calculation of Stark linewidths from electron-ion collisions for the 2s1/2-2p1/2,3/2, λ=2066 and 2067 Å, resonance transitions in B III. The results confirm previous quantum-mechanical R-matrix calculations, but contradict recent measurements and semiclassical and some semiempirical calculations. The differences between the calculations can be attributed to the dominance of small L partial waves in the electron-atom scattering, while the large Stark widths inferred from the measurements would be substantially reduced if allowance is made for hydrodynamic turbulence from high-Reynolds-number flows and the associated Doppler broadening.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

The Scales of Time, Length, Mass, Energy, and Other Fundamental Physical Quantities in the Atomic World and the Use of Atomic Units in Quantum Mechanical Calculations

ERIC Educational Resources Information Center

Teo, Boon K.; Li, Wai-Kee

2011-01-01

This article is divided into two parts. In the first part, the atomic unit (au) system is introduced and the scales of time, space (length), and speed, as well as those of mass and energy, in the atomic world are discussed. In the second part, the utility of atomic units in quantum mechanical and spectroscopic calculations is illustrated with…

Statistical mechanics based on fractional classical and quantum mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Korichi, Z.; Meftah, M. T., E-mail: mewalid@yahoo.com

2014-03-15

The purpose of this work is to study some problems in statistical mechanics based on the fractional classical and quantum mechanics. At first stage we have presented the thermodynamical properties of the classical ideal gas and the system of N classical oscillators. In both cases, the Hamiltonian contains fractional exponents of the phase space (position and momentum). At the second stage, in the context of the fractional quantum mechanics, we have calculated the thermodynamical properties for the black body radiation, studied the Bose-Einstein statistics with the related problem of the condensation and the Fermi-Dirac statistics.

False vacuum decay in quantum mechanics and four dimensional scalar field theory

NASA Astrophysics Data System (ADS)

Bezuglov, Maxim

2018-04-01

When the Higgs boson was discovered in 2012 it was realized that electroweak vacuum may suffer a possible metastability on the Planck scale and can eventually decay. To understand this problem it is important to have reliable predictions for the vacuum decay rate within the framework of quantum field theory. For now, it can only be done at one loop level, which is apparently is not enough. The aim of this work is to develop a technique for the calculation of two and higher order radiative corrections to the false vacuum decay rate in the framework of four dimensional scalar quantum field theory and then apply it to the case of the Standard Model. To achieve this goal, we first start from the case of d=1 dimensional QFT i.e. quantum mechanics. We show that for some potentials two and three loop corrections can be very important and must be taken into account. Next, we use quantum mechanical example as a template for the general d=4 dimensional theory. In it we are concentrating on the calculations of bounce solution and corresponding Green function in so called thin wall approximation. The obtained Green function is then used as a main ingredient for the calculation of two loop radiative corrections to the false vacuum decay rate.

Direct Simulation Monte Carlo Application of the Three Dimensional Forced Harmonic Oscillator Model

DTIC Science & Technology

2017-12-07

quasi -classical scattering theory [3,4] or trajectory [5] calculations, semiclassical, as well as close-coupled [6,7] or full [8] quantum mechanical...the quasi -classical trajectory (QCT) calculations approach for ab initio modeling of collision processes. The DMS method builds on an earlier work...nu ar y 30 , 2 01 8 | h ttp :// ar c. ai aa .o rg | D O I: 1 0. 25 14 /1 .T 52 28 to directly use quasi -classical or quantum mechanic

Importance of parametrizing constraints in quantum-mechanical variational calculations

NASA Technical Reports Server (NTRS)

Chung, Kwong T.; Bhatia, A. K.

1992-01-01

In variational calculations of quantum mechanics, constraints are sometimes imposed explicitly on the wave function. These constraints, which are deduced by physical arguments, are often not uniquely defined. In this work, the advantage of parametrizing constraints and letting the variational principle determine the best possible constraint for the problem is pointed out. Examples are carried out to show the surprising effectiveness of the variational method if constraints are parameterized. It is also shown that misleading results may be obtained if a constraint is not parameterized.

Resonant electronic excitation energy transfer by Dexter mechanism in the quantum dot system

NASA Astrophysics Data System (ADS)

Samosvat, D. M.; Chikalova-Luzina, O. P.; Vyatkin, V. M.; Zegrya, G. G.

2016-11-01

In present work the energy transfer between quantum dots by the exchange (Dexter) mechanism is analysed. The interdot Coulomb interaction is taken into consideration. It is assumed that the quantum dot-donor and the quantum dot-acceptor are made from the same compound A3B5 and embedded in the matrix of other material creating potential barriers for electron and holes. The dependences of the energy transfer rate on the quantum-dot system parameters are found using the Kane model that provides the most adequate description spectra of semiconductors A3B5. Numerical calculations show that the rate of the energy transfer by Dexter mechanism is comparable to the rate of the energy transfer by electrostatic mechanism at the distances approaching to the contact ones.

Identifying the receptor subtype selectivity of retinoid X and retinoic acid receptors via quantum mechanics.

PubMed

Tsuji, Motonori; Shudo, Koichi; Kagechika, Hiroyuki

2017-03-01

Understanding and identifying the receptor subtype selectivity of a ligand is an important issue in the field of drug discovery. Using a combination of classical molecular mechanics and quantum mechanical calculations, this report assesses the receptor subtype selectivity for the human retinoid X receptor (hRXR) and retinoic acid receptor (hRAR) ligand-binding domains (LBDs) complexed with retinoid ligands. The calculated energies show good correlation with the experimentally reported binding affinities. The technique proposed here is a promising method as it reveals the origin of the receptor subtype selectivity of selective ligands.

A quantum framework for likelihood ratios

NASA Astrophysics Data System (ADS)

Bond, Rachael L.; He, Yang-Hui; Ormerod, Thomas C.

The ability to calculate precise likelihood ratios is fundamental to science, from Quantum Information Theory through to Quantum State Estimation. However, there is no assumption-free statistical methodology to achieve this. For instance, in the absence of data relating to covariate overlap, the widely used Bayes’ theorem either defaults to the marginal probability driven “naive Bayes’ classifier”, or requires the use of compensatory expectation-maximization techniques. This paper takes an information-theoretic approach in developing a new statistical formula for the calculation of likelihood ratios based on the principles of quantum entanglement, and demonstrates that Bayes’ theorem is a special case of a more general quantum mechanical expression.

Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface.

PubMed

Li, Hongzhi; Yang, Wei

2007-03-21

An approach is developed in the replica exchange framework to enhance conformational sampling for the quantum mechanical (QM) potential based molecular dynamics simulations. Importantly, with our enhanced sampling treatment, a decent convergence for electronic structure self-consistent-field calculation is robustly guaranteed, which is made possible in our replica exchange design by avoiding direct structure exchanges between the QM-related replicas and the activated (scaled by low scaling parameters or treated with high "effective temperatures") molecular mechanical (MM) replicas. Although the present approach represents one of the early efforts in the enhanced sampling developments specifically for quantum mechanical potentials, the QM-based simulations treated with the present technique can possess the similar sampling efficiency to the MM based simulations treated with the Hamiltonian replica exchange method (HREM). In the present paper, by combining this sampling method with one of our recent developments (the dual-topology alchemical HREM approach), we also introduce a method for the sampling enhanced QM-based free energy calculations.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 4-acetylpyridine

NASA Astrophysics Data System (ADS)

Atilgan, A.; Yurdakul, Ş.; Erdogdu, Y.; Güllüoğlu, M. T.

2018-06-01

The spectroscopic (UV-Vis and infrared), structural and some electronic property observations of the 4-acetylpyridine (4-AP) were reported, which are investigated by using some spectral methods and DFT calculations. FT-IR spectra were obtained for 4-AP at room temperature in the region 4000 cm-1- 400 cm-1. In the DFT calculations, the B3LYP functional with 6-311G++G(d,p) basis set was applied to carry out the quantum mechanical calculations. The Fourier Transform Infrared (FT-IR) and FT-Raman spectra were interpreted by using of normal coordinate analysis based on scaled quantum mechanical force field. The present work expands our understanding of the both the vibrational and structural properties as well as some electronic properties of the 4-AP by means of the theoretical and experimental methods.

Vibrational energy transport in acetylbenzonitrile described by an ab initio-based quantum tier model

NASA Astrophysics Data System (ADS)

Fujisaki, Hiroshi; Yagi, Kiyoshi; Kikuchi, Hiroto; Takami, Toshiya; Stock, Gerhard

2017-01-01

Performing comprehensive quantum-chemical calculations, a vibrational Hamiltonian of acetylbenzonitrile is constructed, on the basis of which a quantum-mechanical "tier model" is developed that describes the vibrational dynamics following excitation of the CN stretch mode. Taking into account 36 vibrational modes and cubic and quartic anharmonic couplings between up to three different modes, the tier model calculations are shown to qualitatively reproduce the main findings of the experiments of Rubtsov and coworkers (2011), including the energy relaxation of the initially excited CN mode and the structure-dependent vibrational transport. Moreover, the calculations suggest that the experimentally measured cross-peak among the CN and CO modes does not correspond to direct excitation of the CO normal mode but rather reflects excited low-frequency vibrations that anharmonically couple to the CO mode. Complementary quasiclassical trajectory calculations are found to be in good overall agreement with the quantum calculations.

A universal test for gravitational decoherence

PubMed Central

Pfister, C.; Kaniewski, J.; Tomamichel, M.; Mantri, A.; Schmucker, R.; McMahon, N.; Milburn, G.; Wehner, S.

2016-01-01

Quantum mechanics and the theory of gravity are presently not compatible. A particular question is whether gravity causes decoherence. Several models for gravitational decoherence have been proposed, not all of which can be described quantum mechanically. Since quantum mechanics may need to be modified, one may question the use of quantum mechanics as a calculational tool to draw conclusions from the data of experiments concerning gravity. Here we propose a general method to estimate gravitational decoherence in an experiment that allows us to draw conclusions in any physical theory where the no-signalling principle holds, even if quantum mechanics needs to be modified. As an example, we propose a concrete experiment using optomechanics. Our work raises the interesting question whether other properties of nature could similarly be established from experimental observations alone—that is, without already having a rather well-formed theory of nature to make sense of experimental data. PMID:27694976

Combined quantum mechanical and molecular mechanical method for metal-organic frameworks: proton topologies of NU-1000.

PubMed

Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

2018-01-17

Metal-organic frameworks (MOFs) are materials with applications in catalysis, gas separations, and storage. Quantum mechanical (QM) calculations can provide valuable guidance to understand and predict their properties. In order to make the calculations faster, rather than modeling these materials as periodic (infinite) systems, it is useful to construct finite models (called cluster models) and use subsystem methods such as fragment methods or combined quantum mechanical and molecular mechanical (QM/MM) methods. Here we employ a QM/MM methodology to study one particular MOF that has been of widespread interest because of its wide pores and good solvent and thermal stability, namely NU-1000, which contains hexanuclear zirconium nodes and 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy 4- ) linkers. A modified version of the Bristow-Tiana-Walsh transferable force field has been developed to allow QM/MM calculations on NU-1000; we call the new parametrization the NU1T force field. We consider isomeric structures corresponding to various proton topologies of the [Zr 6 (μ 3 -O) 8 O 8 H 16 ] 8+ node of NU-1000, and we compute their relative energies using a QM/MM scheme designed for the present kind of problem. We compared the results to full quantum mechanical (QM) energy calculations and found that the QM/MM models can reproduce the full QM relative energetics (which span a range of 334 kJ mol -1 ) with a mean unsigned deviation (MUD) of only 2 kJ mol -1 . Furthermore, we found that the structures optimized by QM/MM are nearly identical to their full QM optimized counterparts.

Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations.

PubMed

Zou, Yi; Wang, Fang; Wang, Yan; Guo, Wenjie; Zhang, Yihua; Xu, Qiang; Lai, Yisheng

2017-05-05

Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations. Secondly, molecular dynamics (MD) simulations and MM/PBSA free energy calculations were employed to determine the dynamic binding process and crucial residues were confirmed through close contact analysis, hydrogen-bond analysis and binding free energy decomposition calculations. Subsequent quantum mechanics and nonbonding interaction analysis were carried out to provide in-depth explanations on the critical role of those key residues, and Arg231 and 7-propionate of the heme group were major contributors to ligand binding, which lowed a great amount of interaction energy. We anticipate that these findings will be valuable for enzymatic studies and rational drug design. Copyright © 2017. Published by Elsevier Masson SAS.

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

PubMed

Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

2015-03-05

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

Assignment of absolute stereostructures through quantum mechanics electronic and vibrational circular dichroism calculations.

PubMed

Dai, Peng; Jiang, Nan; Tan, Ren-Xiang

2016-01-01

Elucidation of absolute configuration of chiral molecules including structurally complex natural products remains a challenging problem in organic chemistry. A reliable method for assigning the absolute stereostructure is to combine the experimental circular dichroism (CD) techniques such as electronic and vibrational CD (ECD and VCD), with quantum mechanics (QM) ECD and VCD calculations. The traditional QM methods as well as their continuing developments make them more applicable with accuracy. Taking some chiral natural products with diverse conformations as examples, this review describes the basic concepts and new developments of QM approaches for ECD and VCD calculations in solution and solid states.

Simulation Of Wave Function And Probability Density Of Modified Poschl Teller Potential Derived Using Supersymmetric Quantum Mechanics

NASA Astrophysics Data System (ADS)

Angraini, Lily Maysari; Suparmi, Variani, Viska Inda

2010-12-01

SUSY quantum mechanics can be applied to solve Schrodinger equation for high dimensional system that can be reduced into one dimensional system and represented in lowering and raising operators. Lowering and raising operators can be obtained using relationship between original Hamiltonian equation and the (super) potential equation. In this paper SUSY quantum mechanics is used as a method to obtain the wave function and the energy level of the Modified Poschl Teller potential. The graph of wave function equation and probability density is simulated by using Delphi 7.0 programming language. Finally, the expectation value of quantum mechanics operator could be calculated analytically using integral form or probability density graph resulted by the programming.

Spin Lifetimes in III-V Semiconductor Heterostructures Originating from Zincblende Symmetry

NASA Astrophysics Data System (ADS)

Lau, Wayne; Olesberg, Jon; Flatté, Michael

2000-03-01

Electron spin relaxation in zincblende type semiconductors at room temperature is dominated by the D'yakonov-Perel' mechanism (DP), which is a direct result of the spin splitting of the conduction band due to the bulk inversion asymmetry (BIA) of zincblende materials. To accurately describe the DP spin relaxation mechanism in quantum wells we employ a heterostructure model based on a fourteen bulk band basis, which accounts for the zincblende symmetry of the heterostructure constituents. Electron spin lifetimes are calculated for 75Å n-doped GaAs/Al_0.4Ga_0.6As quantum wells at room temperature. Excellent agreement between theory and experiments is found. In contrast, the calculated spin lifetimes based on the D'yakonov-Kachorovskii theory are an order magnitude shorter than the experimental values. The spin splitting and spin lifetime in no common atom In_0.53Ga_0.47As/InP quantum wells are also investigated. The contribution to the conduction subband spin splitting is dominated by the native interface asymmetry (NIA) mechanism for thin quantum wells; while the spin splitting is governed by the BIA mechanism for thick quantum wells. We find that BIA provides a satisfactory explanation for the spin lifetime measured in an In_0.53Ga_0.47As/InP quantum well with a 97Å barrier and a 70Å well at room temperature.

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

PubMed

Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

2015-04-14

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamada, Atsushi; Kojima, Hidekazu; Okazaki, Susumu, E-mail: okazaki@apchem.nagoya-u.ac.jp

2014-08-28

In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfermore » process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps{sup −1}, which is about 2.5 times faster than that in vacuum, 0.27 ps{sup −1}. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction.« less

Computational comparison of quantum-mechanical models for multistep direct reactions

NASA Astrophysics Data System (ADS)

Koning, A. J.; Akkermans, J. M.

1993-02-01

We have carried out a computational comparison of all existing quantum-mechanical models for multistep direct (MSD) reactions. The various MSD models, including the so-called Feshbach-Kerman-Koonin, Tamura-Udagawa-Lenske and Nishioka-Yoshida-Weidenmüller models, have been implemented in a single computer system. All model calculations thus use the same set of parameters and the same numerical techniques; only one adjustable parameter is employed. The computational results have been compared with experimental energy spectra and angular distributions for several nuclear reactions, namely, 90Zr(p,p') at 80 MeV, 209Bi(p,p') at 62 MeV, and 93Nb(n,n') at 25.7 MeV. In addition, the results have been compared with the Kalbach systematics and with semiclassical exciton model calculations. All quantum MSD models provide a good fit to the experimental data. In addition, they reproduce the systematics very well and are clearly better than semiclassical model calculations. We furthermore show that the calculated predictions do not differ very strongly between the various quantum MSD models, leading to the conclusion that the simplest MSD model (the Feshbach-Kerman-Koonin model) is adequate for the analysis of experimental data.

Modeling Stretching Modes of Common Organic Molecules with the Quantum Mechanical Harmonic Oscillator: An Undergraduate Vibrational Spectroscopy Laboratory Exercise

ERIC Educational Resources Information Center

Parnis, J. Mark; Thompson, Matthew G. K.

2004-01-01

An introductory undergraduate physical organic chemistry exercise that introduces the harmonic oscillator's use in vibrational spectroscopy is developed. The analysis and modeling exercise begins with the students calculating the stretching modes of common organic molecules with the help of the quantum mechanical harmonic oscillator (QMHO) model.

Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling.

PubMed

Lodola, Alessio; Mor, Marco; Sirirak, Jitnapa; Mulholland, Adrian J

2009-04-01

FAAH (fatty acid amide hydrolase) is a promising target for the treatment of several central nervous system and peripheral disorders. Combined QM/MM (quantum mechanics/molecular mechanics) calculations have elucidated the role of its unusual catalytic triad in the hydrolysis of oleamide and oleoylmethyl ester substrates, and have identified the productive inhibitor-binding orientation for the carbamoylating compound URB524. These are potentially crucial insights for designing new covalent inhibitors of this drug target.

Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives.

PubMed

Rokob, Tibor András; Srnec, Martin; Rulíšek, Lubomír

2012-05-21

In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum-classical approximation. II. Proton transfer reaction in non-polar solvent

NASA Astrophysics Data System (ADS)

Kojima, H.; Yamada, A.; Okazaki, S.

2015-05-01

The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum-classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute-solvent interactions.

Superpersistent Currents in Dirac Fermion Systems

DTIC Science & Technology

2017-03-06

development of quantum mechanics,, but also to quantum information processing and computing . Exploiting various physical systems to realize two-level...Here, using the QSD method, we calculated the dynamical trajectories of the system in the quantum regime. Our computations extending to the long time...currents in 2D Dirac material systems and pertinent phenomena in the emerging field of relativistic quantum nonlinear dynamics and chaos. Systematic

The path integral on the Poincaré upper half plane and for Liouville quantum mechanics

NASA Astrophysics Data System (ADS)

Grosche, C.; Steiner, F.

1987-08-01

We present a rigorous path integral treatment of free motion on the Poincaré upper half plane. The Poincaré upper half plane, as a riemannian manifold, has recently become important in string theory and in the theory of quantum chaos. The calculation is done by a time-transformation and the use of the canonical method for determining quantum corrections to the classical lagrangian. Furthermore, we shall show that the same method also works for Liouville quantum mechanics. In both cases, the energy spectrum and the normalized wavefunctions are determined.

Variational method for calculating the binding energy of the base state of an impurity D- centered on a quantum dot of GaAs-Ga1-xAlxAs

NASA Astrophysics Data System (ADS)

Durán-Flórez, F.; Caicedo, L. C.; Gonzalez, J. E.

2018-04-01

In quantum mechanics it is very difficult to obtain exact solutions, therefore, it is necessary to resort to tools and methods that facilitate the calculations of the solutions of these systems, one of these methods is the variational method that consists in proposing a wave function that depend on several parameters that are adjusted to get close to the exact solution. Authors in the past have performed calculations applying this method using exponential and Gaussian orbital functions with linear and quadratic correlation factors. In this paper, a Gaussian function with a linear correlation factor is proposed, for the calculation of the binding energy of an impurity D ‑ centered on a quantum dot of radius r, the Gaussian function is dependent on the radius of the quantum dot.

Quantum mechanical calculations of vibrational population inversion in chemical reactions - Numerically exact L-squared-amplitude-density study of the H2Br reactive system

NASA Technical Reports Server (NTRS)

Zhang, Y. C.; Zhang, J. Z. H.; Kouri, D. J.; Haug, K.; Schwenke, D. W.

1988-01-01

Numerically exact, fully three-dimensional quantum mechanicl reactive scattering calculations are reported for the H2Br system. Both the exchange (H + H-prime Br to H-prime + HBr) and abstraction (H + HBR to H2 + Br) reaction channels are included in the calculations. The present results are the first completely converged three-dimensional quantum calculations for a system involving a highly exoergic reaction channel (the abstraction process). It is found that the production of vibrationally hot H2 in the abstraction reaction, and hence the extent of population inversion in the products, is a sensitive function of initial HBr rotational state and collision energy.

Bond order potential module for LAMMPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

2012-09-11

pair_bop is a module for performing energy calculations using the Bond Order Potential (BOP) for use in the parallel molecular dynamics code LAMMPS. The bop pair style computes BOP based upon quantum mechanical incorporating both sigma and pi bondings. By analytically deriving the BOP pair bop from quantum mechanical theory its transferability to different phases can approach that of quantum mechanical methods. This potential is extremely effective at modeling 111-V and II-VI compounds such as GaAs and CdTe. This potential is similar to the original BOP developed by Pettifor and later updated by Murdock et al. and Ward et al.

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

PubMed

Ferenczy, György G

2013-04-05

Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods. Copyright © 2012 Wiley Periodicals, Inc.

Quantum statistical mechanics of dense partially ionized hydrogen.

NASA Technical Reports Server (NTRS)

Dewitt, H. E.; Rogers, F. J.

1972-01-01

The theory of dense hydrogenic plasmas beginning with the two component quantum grand partition function is reviewed. It is shown that ionization equilibrium and molecular dissociation equilibrium can be treated in the same manner with proper consideration of all two-body states. A quantum perturbation expansion is used to give an accurate calculation of the equation of state of the gas for any degree of dissociation and ionization. In this theory, the effective interaction between any two charges is the dynamic screened potential obtained from the plasma dielectric function. We make the static approximation; and we carry out detailed numerical calculations with the bound and scattering states of the Debye potential, using the Beth-Uhlenbeck form of the quantum second virial coefficient. We compare our results with calculations from the Saha equation.

Semiclassical treatment of fusion and breakup processes of ^{6,8}He halo nuclei

NASA Astrophysics Data System (ADS)

Majeed, Fouad A.; Abdul-Hussien, Yousif A.

2016-06-01

A semiclassical approach has been used to study the effect of channel coupling on the calculations of the total fusion reaction cross section σ _{fus}, and the fusion barrier distribution D_{fus} for the systems 6He +^{238}U and 8He +^{197}Au. Since these systems invloves light exotic nuclei, breakup states channel play an important role that should be considered in the calculations. In semiclassical treatment, the relative motion between the projectile and target nuclei is approximated by a classical trajectory while the intrinsic dynamics is handled by time-dependent quantum mechanics. The calculations of the total fusion cross section σ _{fus}, and the fusion barrier distribution D_{fus} are compared with the full quantum mechanical calculations using the coupled-channels calculations with all order coupling using the computer code and with the available experimental data.

A QUANTUM MECHANICAL STUDY OF THE PROTONATION AND COVALENT HYDRATION OF QUINAZOLINE IN THE PRESENCE OF METAL CATIONS

EPA Science Inventory

We have investigated the protonation and reversible covalent hydration of quinazoline in the presence of Li+, Na+, and Ca2+ ions using ab initio quantum mechanical calculations at the MP2/6-31G**//HF/6-31G*level of theory. Proton affinities, enthalpies of hydration at 298.15K (DH...

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

PubMed Central

2015-01-01

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

DOE PAGES

Sodt, Alexander J.; Mei, Ye; Konig, Gerhard; ...

2014-10-16

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completelymore » avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.« less

Theoretical study of dynamic electron-spin-polarization via the doublet-quartet quantum-mixed state and time-resolved ESR spectra of the quartet high-spin state.

PubMed

Teki, Yoshio; Matsumoto, Takafumi

2011-04-07

The mechanism of the unique dynamic electron polarization of the quartet (S = 3/2) high-spin state via a doublet-quartet quantum-mixed state and detail theoretical calculations of the population transfer are reported. By the photo-induced electron transfer, the quantum-mixed charge-separate state is generated in acceptor-donor-radical triad (A-D-R). This mechanism explains well the unique dynamic electron polarization of the quartet state of A-D-R. The generation of the selectively populated quantum-mixed state and its transfer to the strongly coupled pure quartet and doublet states have been treated both by a perturbation approach and by exact numerical calculations. The analytical solutions show that generation of the quantum-mixed states with the selective populations after de-coherence and/or accompanying the (complete) dephasing during the charge-recombination are essential for the unique dynamic electron polarization. Thus, the elimination of the quantum coherence (loss of the quantum information) is the key process for the population transfer from the quantum-mixed state to the quartet state. The generation of high-field polarization on the strongly coupled quartet state by the charge-recombination process can be explained by a polarization transfer from the quantum-mixed charge-separate state. Typical time-resolved ESR patterns of the quantum-mixed state and of the strongly coupled quartet state are simulated based on the generation mechanism of the dynamic electron polarization. The dependence of the spectral pattern of the quartet high-spin state has been clarified for the fine-structure tensor and the exchange interaction of the quantum-mixed state. The spectral pattern of the quartet state is not sensitive towards the fine-structure tensor of the quantum-mixed state, because this tensor contributes only as a perturbation in the population transfer to the spin-sublevels of the quartet state. Based on the stochastic Liouville equation, it is also discussed why the selective population in the quantum-mixed state is generated for the "finite field" spin-sublevels. The numerical calculations of the elimination of the quantum coherence (de-coherence and/or dephasing) are demonstrated. A new possibility of the enhanced intersystem crossing pathway in solution is also proposed.

Stereodynamics in NO(X) + Ar inelastic collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brouard, M., E-mail: mark.brouard@chem.ox.ac.uk; Chadwick, H.; Gordon, S. D. S.

2016-06-14

The effect of orientation of the NO(X) bond axis prior to rotationally inelastic collisions with Ar has been investigated experimentally and theoretically. A modification to conventional velocity-map imaging ion optics is described, which allows the orientation of hexapole state-selected NO(X) using a static electric field, followed by velocity map imaging of the resonantly ionized scattered products. Bond orientation resolved differential cross sections are measured experimentally for a series of spin-orbit conserving transitions and compared with quantum mechanical calculations. The agreement between experimental results and those from quantum mechanical calculations is generally good. Parity pairs, which have previously been observed inmore » collisions of unpolarized NO with various rare gases, are not observed due to the coherent superposition of the two j = 1/2, Ω = 1/2 Λ-doublet levels in the orienting field. The normalized difference differential cross sections are found to depend predominantly on the final rotational state, and are not very sensitive to the final Λ-doublet level. The differential steric effect has also been investigated theoretically, by means of quantum mechanical and classical calculations. Classically, the differential steric effect can be understood by considering the steric requirement for different types of trajectories that contribute to different regions of the differential cross section. However, classical effects cannot account quantitatively for the differential steric asymmetry observed in NO(X) + Ar collisions, which reflects quantum interference from scattering at either end of the molecule. This quantum interference effect is dominated by the repulsive region of the potential.« less

Quantum Mechanical Calculations of Cytosine, Thiocytosine and Their Radical Ions

NASA Astrophysics Data System (ADS)

Singh, Rashmi

2010-08-01

The RNA and DNA are polymer that share some interesting similarities, for instance it is well known that cytosine is the one of the common nucleic acid base. The sulfur is characterized as a very reactive element and it has been used, in chemical warfare agents. Since the genetic information is based on the sequence of the nucleic acid bases. The quantum mechanical calculations of the energies, geometries, charges and vibrational characteristics of the cytosine and thiocytosine. and their corresponding radicals were carried out by using DFT method with b3lyp/6-311++g** basis set.

Non-perturbative background field calculations

NASA Astrophysics Data System (ADS)

Stephens, C. R.

1988-01-01

New methods are developed for calculating one loop functional determinants in quantum field theory. Instead of relying on a calculation of all the eigenvalues of the small fluctuation equation, these techniques exploit the ability of the proper time formalism to reformulate an infinite dimensional field theoretic problem into a finite dimensional covariant quantum mechanical analog, thereby allowing powerful tools such as the method of Jacobi fields to be used advantageously in a field theory setting. More generally the methods developed herein should be extremely valuable when calculating quantum processes in non-constant background fields, offering a utilitarian alternative to the two standard methods of calculation—perturbation theory in the background field or taking the background field into account exactly. The formalism developed also allows for the approximate calculation of covariances of partial differential equations from a knowledge of the solutions of a homogeneous ordinary differential equation.

Quantum calculations of the carrier mobility: Methodology, Matthiessen's rule, and comparison with semi-classical approaches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niquet, Yann-Michel, E-mail: yniquet@cea.fr; Nguyen, Viet-Hung; Duchemin, Ivan

2014-02-07

We discuss carrier mobilities in the quantum Non-Equilibrium Green's Functions (NEGF) framework. We introduce a method for the extraction of the mobility that is free from contact resistance contamination and with minimal needs for ensemble averages. We focus on silicon thin films as an illustration, although the method can be applied to various materials such as semiconductor nanowires or carbon nanostructures. We then introduce a new paradigm for the definition of the partial mobility μ{sub M} associated with a given elastic scattering mechanism “M,” taking phonons (PH) as a reference (μ{sub M}{sup −1}=μ{sub PH+M}{sup −1}−μ{sub PH}{sup −1}). We argue thatmore » this definition makes better sense in a quantum transport framework as it is free from long range interference effects that can appear in purely ballistic calculations. As a matter of fact, these mobilities satisfy Matthiessen's rule for three mechanisms [e.g., surface roughness (SR), remote Coulomb scattering (RCS) and phonons] much better than the usual, single mechanism calculations. We also discuss the problems raised by the long range spatial correlations in the RCS disorder. Finally, we compare semi-classical Kubo-Greenwood (KG) and quantum NEGF calculations. We show that KG and NEGF are in reasonable agreement for phonon and RCS, yet not for SR. We discuss the reasons for these discrepancies.« less

Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

PubMed

Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao

2013-09-10

Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

Squeezed cooling of mechanical motion beyond the resolved-sideband limit

NASA Astrophysics Data System (ADS)

Yang, Cheng; Zhang, Lin; Zhang, Weiping

2018-04-01

Cavity optomechanics provides a unique platform for controlling micromechanical systems by means of optical fields that cross the classical-quantum boundary to achieve solid foundations for quantum technologies. Currently, optomechanical resonators have become promising candidates for the development of precisely controlled nano-motors, ultrasensitive sensors and robust quantum information processors. For all these applications, a crucial requirement is to cool the mechanical resonators down to their quantum ground states. In this paper, we present a novel cooling scheme to further cool a micromechanical resonator via the noise squeezing effect. One quadrature in such a resonator can be squeezed to induce enhanced fluctuations in the other, “heated” quadrature, which can then be used to cool the mechanical motion via conventional optomechanical coupling. Our theoretical analysis and numerical calculations demonstrate that this squeeze-and-cool mechanism offers a quick technique for deeply cooling a macroscopic mechanical resonator to an unprecedented temperature region below the zero-point fluctuations.

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution.

PubMed

Liu, Peng; Wang, Qiong; Niu, Meixing; Wang, Dunyou

2017-08-10

Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.

Probing finite coarse-grained virtual Feynman histories with sequential weak values

NASA Astrophysics Data System (ADS)

Georgiev, Danko; Cohen, Eliahu

2018-05-01

Feynman's sum-over-histories formulation of quantum mechanics has been considered a useful calculational tool in which virtual Feynman histories entering into a coherent quantum superposition cannot be individually measured. Here we show that sequential weak values, inferred by consecutive weak measurements of projectors, allow direct experimental probing of individual virtual Feynman histories, thereby revealing the exact nature of quantum interference of coherently superposed histories. Because the total sum of sequential weak values of multitime projection operators for a complete set of orthogonal quantum histories is unity, complete sets of weak values could be interpreted in agreement with the standard quantum mechanical picture. We also elucidate the relationship between sequential weak values of quantum histories with different coarse graining in time and establish the incompatibility of weak values for nonorthogonal quantum histories in history Hilbert space. Bridging theory and experiment, the presented results may enhance our understanding of both weak values and quantum histories.

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism.

PubMed

Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

2016-10-11

The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S N 1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

Wave packet and statistical quantum calculations for the He + NeH⁺ → HeH⁺ + Ne reaction on the ground electronic state.

PubMed

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N

2014-09-21

A real wave packet based time-dependent method and a statistical quantum method have been used to study the He + NeH(+) (v, j) reaction with the reactant in various ro-vibrational states, on a recently calculated ab initio ground state potential energy surface. Both the wave packet and statistical quantum calculations were carried out within the centrifugal sudden approximation as well as using the exact Hamiltonian. Quantum reaction probabilities exhibit dense oscillatory pattern for smaller total angular momentum values, which is a signature of resonances in a complex forming mechanism for the title reaction. Significant differences, found between exact and approximate quantum reaction cross sections, highlight the importance of inclusion of Coriolis coupling in the calculations. Statistical results are in fairly good agreement with the exact quantum results, for ground ro-vibrational states of the reactant. Vibrational excitation greatly enhances the reaction cross sections, whereas rotational excitation has relatively small effect on the reaction. The nature of the reaction cross section curves is dependent on the initial vibrational state of the reactant and is typical of a late barrier type potential energy profile.

Efficient free energy calculations of quantum systems through computer simulations

NASA Astrophysics Data System (ADS)

Antonelli, Alex; Ramirez, Rafael; Herrero, Carlos; Hernandez, Eduardo

2009-03-01

In general, the classical limit is assumed in computer simulation calculations of free energy. This approximation, however, is not justifiable for a class of systems in which quantum contributions for the free energy cannot be neglected. The inclusion of quantum effects is important for the determination of reliable phase diagrams of these systems. In this work, we present a new methodology to compute the free energy of many-body quantum systems [1]. This methodology results from the combination of the path integral formulation of statistical mechanics and efficient non-equilibrium methods to estimate free energy, namely, the adiabatic switching and reversible scaling methods. A quantum Einstein crystal is used as a model to show the accuracy and reliability the methodology. This new method is applied to the calculation of solid-liquid coexistence properties of neon. Our findings indicate that quantum contributions to properties such as, melting point, latent heat of fusion, entropy of fusion, and slope of melting line can be up to 10% of the calculated values using the classical approximation. [1] R. M. Ramirez, C. P. Herrero, A. Antonelli, and E. R. Hernández, Journal of Chemical Physics 129, 064110 (2008)

Intraband light absorption by holes in InGaAsP/InP quantum wells

NASA Astrophysics Data System (ADS)

Pavlov, N. V.; Zegrya, G. G.

2018-03-01

A microscopic analysis of the mechanism of intraband radiation absorption by holes with their transition to a spin-split band for quantum wells based on InGaAsP/InP solid solutions is performed within the framework of the four-band Kane model. The calculation is made for two polarizations of the incident radiation: along the crystal growth axis and in the plane of the quantum well. It is shown that this process can be the main mechanism of internal radiation losses for quantum well lasers. It is also shown that the dependence of the absorption coefficient on the width of the quantum well has a maximum at a well width from 40 to 60 A.

Spin relaxation in quantum dots due to electron exchange with leads.

PubMed

Vorontsov, A B; Vavilov, M G

2008-11-28

We calculate spin relaxation rates in lateral quantum dot systems due to electron exchange between dots and leads. Using rate equations, we develop a theoretical description of the experimentally observed electric current in the spin blockade regime of double quantum dots. A single expression fits the entire current profile and describes the structure of both the conduction peaks and the suppressed ("valley") region. Extrinsic rates calculated here have to be taken into account for accurate extraction of intrinsic relaxation rates due to the spin-orbit and hyperfine spin scattering mechanisms from spin blockade measurements.

Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco

2016-09-13

The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xianwei; State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062; Zhang, John Z. H.

2015-11-14

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. Inmore » this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.« less

An approach for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics. II. Thermal correlation functions.

PubMed

Liu, Jian; Miller, William H

2011-03-14

We show the exact expression of the quantum mechanical time correlation function in the phase space formulation of quantum mechanics. The trajectory-based dynamics that conserves the quantum canonical distribution-equilibrium Liouville dynamics (ELD) proposed in Paper I is then used to approximately evaluate the exact expression. It gives exact thermal correlation functions (of even nonlinear operators, i.e., nonlinear functions of position or momentum operators) in the classical, high temperature, and harmonic limits. Various methods have been presented for the implementation of ELD. Numerical tests of the ELD approach in the Wigner or Husimi phase space have been made for a harmonic oscillator and two strongly anharmonic model problems, for each potential autocorrelation functions of both linear and nonlinear operators have been calculated. It suggests ELD can be a potentially useful approach for describing quantum effects for complex systems in condense phase.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donangelo, R.J.

An integral representation for the classical limit of the quantum mechanical S-matrix is developed and applied to heavy-ion Coulomb excitation and Coulomb-nuclear interference. The method combines the quantum principle of superposition with exact classical dynamics to describe the projectile-target system. A detailed consideration of the classical trajectories and of the dimensionless parameters that characterize the system is carried out. The results are compared, where possible, to exact quantum mechanical calculations and to conventional semiclassical calculations. It is found that in the case of backscattering the classical limit S-matrix method is able to almost exactly reproduce the quantum-mechanical S-matrix elements, andmore » therefore the transition probabilities, even for projectiles as light as protons. The results also suggest that this approach should be a better approximation for heavy-ion multiple Coulomb excitation than earlier semiclassical methods, due to a more accurate description of the classical orbits in the electromagnetic field of the target nucleus. Calculations using this method indicate that the rotational excitation probabilities in the Coulomb-nuclear interference region should be very sensitive to the details of the potential at the surface of the nucleus, suggesting that heavy-ion rotational excitation could constitute a sensitive probe of the nuclear potential in this region. The application to other problems as well as the present limits of applicability of the formalism are also discussed.« less

Quantum biological channel modeling and capacity calculation.

PubMed

Djordjevic, Ivan B

2012-12-10

Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general.

Efficient approach to obtain free energy gradient using QM/MM MD simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asada, Toshio; Koseki, Shiro; The Research Institute for Molecular Electronic Devices

2015-12-31

The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means ofmore » FEG and the nudged elastic band (NEB) method.« less

Simulation of wave packet tunneling of interacting identical particles

NASA Astrophysics Data System (ADS)

Lozovik, Yu. E.; Filinov, A. V.; Arkhipov, A. S.

2003-02-01

We demonstrate a different method of simulation of nonstationary quantum processes, considering the tunneling of two interacting identical particles, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based on the Wigner representation of quantum mechanics. In the context of this method ensembles of classical trajectories are used to solve quantum Wigner-Liouville equation. These classical trajectories obey Hamiltonian-like equations, where the effective potential consists of the usual classical term and the quantum term, which depends on the Wigner function and its derivatives. The quantum term is calculated using local distribution of trajectories in phase space, therefore, classical trajectories are not independent, contrary to classical molecular dynamics. The developed WMD method takes into account the influence of exchange and interaction between particles. The role of direct and exchange interactions in tunneling is analyzed. The tunneling times for interacting particles are calculated.

Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertoni, Colleen

Computational chemistry uses the theoretical advances of quantum mechanics and the algorithmic and hardware advances of computer science to give insight into chemical problems. It is currently possible to do highly accurate quantum chemistry calculations, but the most accurate methods are very computationally expensive. Thus it is only feasible to do highly accurate calculations on small molecules, since typically more computationally efficient methods are also less accurate. The overall goal of my dissertation work has been to try to decrease the computational expense of calculations without decreasing the accuracy. In particular, my dissertation work focuses on fragmentation methods, intermolecular interactionsmore » methods, analytic gradients, and taking advantage of new hardware.« less

Density of Trap States and Auger-mediated Electron Trapping in CdTe Quantum-Dot Solids.

PubMed

Boehme, Simon C; Azpiroz, Jon Mikel; Aulin, Yaroslav V; Grozema, Ferdinand C; Vanmaekelbergh, Daniël; Siebbeles, Laurens D A; Infante, Ivan; Houtepen, Arjan J

2015-05-13

Charge trapping is an ubiquitous process in colloidal quantum-dot solids and a major limitation to the efficiency of quantum dot based devices such as solar cells, LEDs, and thermoelectrics. Although empirical approaches led to a reduction of trapping and thereby efficiency enhancements, the exact chemical nature of the trapping mechanism remains largely unidentified. In this study, we determine the density of trap states in CdTe quantum-dot solids both experimentally, using a combination of electrochemical control of the Fermi level with ultrafast transient absorption and time-resolved photoluminescence spectroscopy, and theoretically, via density functional theory calculations. We find a high density of very efficient electron traps centered ∼0.42 eV above the valence band. Electrochemical filling of these traps increases the electron lifetime and the photoluminescence quantum yield by more than an order of magnitude. The trapping rate constant for holes is an order of magnitude lower that for electrons. These observations can be explained by Auger-mediated electron trapping. From density functional theory calculations we infer that the traps are formed by dicoordinated Te atoms at the quantum dot surface. The combination of our unique experimental determination of the density of trap states with the theoretical modeling of the quantum dot surface allows us to identify the trapping mechanism and chemical reaction at play during charge trapping in these quantum dots.

Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical-Molecular Mechanical Simulations of Proton Transfer in DNA.

PubMed

Das, Susanta; Nam, Kwangho; Major, Dan Thomas

2018-03-13

In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. ±1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

Large enhancement in photocurrent by Mn doping in CdSe/ZTO quantum dot sensitized solar cells.

PubMed

Pimachev, Artem; Poudyal, Uma; Proshchenko, Vitaly; Wang, Wenyong; Dahnovsky, Yuri

2016-09-29

We find a large enhancement in the efficiency of CdSe quantum dot sensitized solar cells by doping with manganese. In the presence of Mn impurities in relatively small concentrations (2.3%) the photoelectric current increases by up to 190%. The average photocurrent enhancement is about 160%. This effect cannot be explained by a light absorption mechanism because the experimental and theoretical absorption spectra demonstrate that there is no change in the absorption coefficient in the presence of the Mn impurities. To explain such a large increase in the injection current we propose a tunneling mechanism of electron injection from the quantum dot LUMO state to the Zn 2 SnO 4 (ZTO) semiconductor photoanode. The calculated enhancement is approximately equal to 150% which is very close to the experimental average value of 160%. The relative discrepancy between the calculated and experimentally measured ratios of the IPCE currents is only 6.25%. For other mechanisms (such as electron trapping, etc.) the remaining 6.25% cannot explain the large change in the experimental IPCE. Thus we have indirectly proved that electron tunneling is the major mechanism of photocurrent enhancement. This work proposes a new approach for a significant improvement in the efficiency of quantum dot sensitized solar cells.

Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanematsu, Yusuke; Tachikawa, Masanori

2014-11-14

Multicomponent quantum mechanical (MC-QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC-QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC-QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC-QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O–H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solventmore » effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC-QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.« less

Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies.

PubMed

Yang, Yang; Culpitt, Tanner; Hammes-Schiffer, Sharon

2018-04-05

The quantum mechanical treatment of both electrons and protons in the calculation of excited state properties is critical for describing nonadiabatic processes such as photoinduced proton-coupled electron transfer. Multicomponent density functional theory enables the consistent quantum mechanical treatment of more than one type of particle and has been implemented previously for studying ground state molecular properties within the nuclear-electronic orbital (NEO) framework, where all electrons and specified protons are treated quantum mechanically. To enable the study of excited state molecular properties, herein the linear response multicomponent time-dependent density functional theory (TDDFT) is derived and implemented within the NEO framework. Initial applications to FHF - and HCN illustrate that NEO-TDDFT provides accurate proton and electron excitation energies within a single calculation. As its computational cost is similar to that of conventional electronic TDDFT, the NEO-TDDFT approach is promising for diverse applications, particularly nonadiabatic proton transfer reactions, which may exhibit mixed electron-proton vibronic excitations.

Computational vibrational study on coordinated nicotinamide

NASA Astrophysics Data System (ADS)

Bolukbasi, Olcay; Akyuz, Sevim

2005-06-01

The molecular structure and vibrational spectra of zinc (II) halide complexes of nicotinamide (ZnX 2(NIA) 2; X=Cl or Br; NIA=Nicotinamide) were investigated by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimisation and vibrational wavenumber calculations of zinc halide complexes of nicotinamide were carried out by using the DFT/RB3LYP level of theory with 6-31G(d,p) basis set. The calculated wavenumbers were scaled by using scaled quantum mechanical (SQM) force field method. The fundamental vibrational modes were characterised by their total energy distribution. The coordination effects on nicotinamide through the ring nitrogen were discussed.

Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

PubMed

Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

2017-07-21

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

PubMed

Tvaroška, Igor

2015-02-11

Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

"Quantum Interference with Slits" Revisited

ERIC Educational Resources Information Center

Rothman, Tony; Boughn, Stephen

2011-01-01

Marcella has presented a straightforward technique employing the Dirac formalism to calculate single- and double-slit interference patterns. He claims that no reference is made to classical optics or scattering theory and that his method therefore provides a purely quantum mechanical description of these experiments. He also presents his…

Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations.

PubMed

Rosnik, Andreana M; Curutchet, Carles

2015-12-08

Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.

A quantum wave based compact modeling approach for the current in ultra-short DG MOSFETs suitable for rapid multi-scale simulations

NASA Astrophysics Data System (ADS)

Hosenfeld, Fabian; Horst, Fabian; Iñíguez, Benjamín; Lime, François; Kloes, Alexander

2017-11-01

Source-to-drain (SD) tunneling decreases the device performance in MOSFETs falling below the 10 nm channel length. Modeling quantum mechanical effects including SD tunneling has gained more importance specially for compact model developers. The non-equilibrium Green's function (NEGF) has become a state-of-the-art method for nano-scaled device simulation in the past years. In the sense of a multi-scale simulation approach it is necessary to bridge the gap between compact models with their fast and efficient calculation of the device current, and numerical device models which consider quantum effects of nano-scaled devices. In this work, an NEGF based analytical model for nano-scaled double-gate (DG) MOSFETs is introduced. The model consists of a closed-form potential solution of a classical compact model and a 1D NEGF formalism for calculating the device current, taking into account quantum mechanical effects. The potential calculation omits the iterative coupling and allows the straightforward current calculation. The model is based on a ballistic NEGF approach whereby backscattering effects are considered as second order effect in a closed-form. The accuracy and scalability of the non-iterative DG MOSFET model is inspected in comparison with numerical NanoMOS TCAD data for various channel lengths. With the help of this model investigations on short-channel and temperature effects are performed.

On classical and quantum dynamics of tachyon-like fields and their cosmological implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dimitrijević, Dragoljub D., E-mail: ddrag@pmf.ni.ac.rs; Djordjević, Goran S., E-mail: ddrag@pmf.ni.ac.rs; Milošević, Milan, E-mail: ddrag@pmf.ni.ac.rs

2014-11-24

We consider a class of tachyon-like potentials, motivated by string theory, D-brane dynamics and inflation theory in the context of classical and quantum mechanics. A formalism for describing dynamics of tachyon fields in spatially homogenous and one-dimensional - classical and quantum mechanical limit is proposed. A few models with concrete potentials are considered. Additionally, possibilities for p-adic and adelic generalization of these models are discussed. Classical actions and corresponding quantum propagators, in the Feynman path integral approach, are calculated in a form invariant on a change of the background number fields, i.e. on both archimedean and nonarchimedean spaces. Looking formore » a quantum origin of inflation, relevance of p-adic and adelic generalizations are briefly discussed.« less

Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

PubMed

Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

2013-02-19

Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of the atom: for an sp(3) carbon atom, we consider the two core 1s electrons and treat that carbon as an atom with three electrons. This results in an LSCF+3 model. Similarly, a nitrogen atom with a lone pair of electrons available for conjugation is treated as an atom with five electrons (LSCF+5). This approach is particularly well suited to splitting peptide bonds and other bonds that include carbon or nitrogen atoms. To embed the induced polarization within the calculation, researchers must use a polarizable force field. However, because the parameters of the usual force fields include an average of the induction effects, researchers typically can obtain satisfactory results without explicitly introducing the polarization. When considering electronic transitions, researchers must take into account the changes in the electronic polarization. One approach is to simulate the electronic cloud of the surroundings by a continuum whose dielectric constant is equal to the square of the refractive index. This Electronic Response of the Surroundings (ERS) methodology allows researchers to model the changes in induced polarization easily. We illustrate this approach by modeling the electronic absorption of tryptophan in human serum albumin (HSA).

Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F- + CH3I reaction in aqueous solution.

PubMed

Liu, Peng; Zhang, Jingxue; Wang, Dunyou

2017-06-07

A double-inversion mechanism of the F - + CH 3 I reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state. The potentials of mean force were calculated with both the DFT/MM and CCSD(T)/MM levels of theory. Our calculated free energy barrier of the abstraction-induced inversion is 69.5 kcal mol -1 at the CCSD(T)/MM level of theory, which agrees with the one at 72.9 kcal mol -1 calculated using the Born solvation model and gas-phase data; and our calculated free energy barrier of the Walden inversion is 24.2 kcal mol -1 , which agrees very well with the experimental value at 25.2 kcal mol -1 in aqueous solution. The calculations show that the aqueous solution makes significant contributions to the potentials of mean force and exerts a big impact on the molecular-level evolution along the reaction pathway.

Temperature equilibration rate with Fermi-Dirac statistics.

PubMed

Brown, Lowell S; Singleton, Robert L

2007-12-01

We calculate analytically the electron-ion temperature equilibration rate in a fully ionized, weakly to moderately coupled plasma, using an exact treatment of the Fermi-Dirac electrons. The temperature is sufficiently high so that the quantum-mechanical Born approximation to the scattering is valid. It should be emphasized that we do not build a model of the energy exchange mechanism, but rather, we perform a systematic first principles calculation of the energy exchange. At the heart of this calculation lies the method of dimensional continuation, a technique that we borrow from quantum field theory and use in a different fashion to regulate the kinetic equations in a consistent manner. We can then perform a systematic perturbation expansion and thereby obtain a finite first-principles result to leading and next-to-leading order. Unlike model building, this systematic calculation yields an estimate of its own error and thus prescribes its domain of applicability. The calculational error is small for a weakly to moderately coupled plasma, for which our result is nearly exact. It should also be emphasized that our calculation becomes unreliable for a strongly coupled plasma, where the perturbative expansion that we employ breaks down, and one must then utilize model building and computer simulations. Besides providing different and potentially useful results, we use this calculation as an opportunity to explain the method of dimensional continuation in a pedagogical fashion. Interestingly, in the regime of relevance for many inertial confinement fusion experiments, the degeneracy corrections are comparable in size to the subleading quantum correction below the Born approximation. For consistency, we therefore present this subleading quantum-to-classical transition correction in addition to the degeneracy correction.

Fluorescence quenching near small metal nanoparticles.

PubMed

Pustovit, V N; Shahbazyan, T V

2012-05-28

We develop a microscopic model for fluorescence of a molecule (or semiconductor quantum dot) near a small metal nanoparticle. When a molecule is situated close to metal surface, its fluorescence is quenched due to energy transfer to the metal. We perform quantum-mechanical calculations of energy transfer rates for nanometer-sized Au nanoparticles and find that nonlocal and quantum-size effects significantly enhance dissipation in metal as compared to those predicted by semiclassical electromagnetic models. However, the dependence of transfer rates on molecule's distance to metal nanoparticle surface, d, is significantly weaker than the d(-4) behavior for flat metal surface with a sharp boundary predicted by previous calculations within random phase approximation.

Modeling Alkyl p-Methoxy Cinnamate (APMC) as UV absorber based on electronic transition using semiempirical quantum mechanics ZINDO/s calculation

NASA Astrophysics Data System (ADS)

Salmahaminati; Azis, Muhlas Abdul; Purwiandono, Gani; Arsyik Kurniawan, Muhammad; Rubiyanto, Dwiarso; Darmawan, Arif

2017-11-01

In this research, modeling several alkyl p-methoxy cinnamate (APMC) based on electronic transition by using semiempirical mechanical quantum ZINDO/s calculation is performed. Alkyl cinnamates of C1 (methyl) up to C7 (heptyl) homolog with 1-5 example structures of each homolog are used as materials. Quantum chemistry-package software Hyperchem 8.0 is used to simulate the drawing of the structure, geometry optimization by a semiempirical Austin Model 1 algorithm and single point calculation employing a semiempirical ZINDO/s technique. ZINDO/s calculations use a defined criteria that singly excited -Configuration Interaction (CI) where a gap of HOMO-LUMO energy transition and maximum degeneracy level are 7 and 2, respectively. Moreover, analysis of the theoretical spectra is focused on the UV-B (290-320 nm) and UV-C (200-290 nm) area. The results show that modeling of the compound can be used to predict the type of UV protection activity depends on the electronic transition in the UV area. Modification of the alkyl homolog relatively does not change the value of wavelength absorption to indicate the UV protection activity. Alkyl cinnamate compounds are predicted as UV-B and UV-C sunscreen.

CARBON-RICH MOLECULAR CHAINS IN PROTOPLANETARY AND PLANETARY ATMOSPHERES: QUANTUM MECHANISMS AND ELECTRON ATTACHMENT RATES FOR ANION FORMATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carelli, F.; Grassi, T.; Gianturco, F. A.

The elementary mechanisms through which molecular polyynes could form stable negative ions after interacting with free electrons in planetary atmospheres (e.g., Titan's) are analyzed using quantum scattering calculations and quantum structure methods. The case of radical species and of nonpolar partners are analyzed via specific examples for both the C{sub n}H and HC{sub n}H series, with n values from 4 to 12. We show that attachment processes to polar radicals are dominating the anionic production and that the mediating role of dipolar scattering states is crucial to their formation. The corresponding attachment rates are presented as calculated upper limits tomore » their likely values and are obtained down to the low temperatures of interest. The effects of the computed rates, when used in simple evolutionary models, are also investigated and presented in detail.« less

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

PubMed

Sevastik, Robin; Himo, Fahmi

2007-12-01

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

Raman spectrum, quantum mechanical calculations and vibrational assignments of (95% alpha-TeO2/5% Sm2O3) glass.

PubMed

Shaltout, I; Mohamed, Tarek A

2007-06-01

Chozen system of tellurite glasses doped with rare earth oxides (95% alpha-TeO(2)+5% Sm2O3) was prepared by melt quenching. Consequently, the Raman spectrum (150-1250 cm(-1)) of the modified tellurite have been recorded. As a continuation to our normal coordinate analysis, force constants and quantum mechanical (QM) calculations for tbp TeO4(4-) (triagonal bipyramid, C(2v)) and TeO(3+1); Te2O7(6-) (bridged tetrahedral), we have carried out ab initio frequency calculations for tpy TeO3(2-) (triagonal pyramidal, C(3v) and C(s)) and tp TeO3(2-) (triagonal planar, D(3h)) ions. The quantum mechanical calculations at the levels of RHF, B3LYP and MP2 allow confident vibrational assignments and structural identification in the binary oxide glass (95% alpha-TeO2 +5% Sm2O3). The dominant three-dimensional network structures in the modified glass are triagonal pyramidal TeO3 with minor features of short range distorted tbp TeO4 and bridged tetrahedral unit of TeO(3+1), leading to a structure of infinite chain. Therefore, alpha-TeO2/Sm2O3 (95/5%) glass experience structural changes from TeO4 (tbp); Te2O7 (TeO(3+1))-->TeO3 (tpy).

I-V characterization of a quantum well infrared photodetector with stepped and graded barriers

NASA Astrophysics Data System (ADS)

Nutku, F.; Erol, A.; Gunes, M.; Buklu, L. B.; Ergun, Y.; Arikan, M. C.

2012-09-01

I-V characterization of an n-type quantum well infrared photodetector which consists of stepped and graded barriers has been done under dark at temperatures between 20-300 K. Different current transport mechanisms and transition between them have been observed at temperature around 47 K. Activation energies of the electrons at various bias voltages have been obtained from the temperature dependent I-V measurements. Activation energy at zero bias has been calculated by extrapolating the bias dependence of the activation energies. Ground state energies and barrier heights of the four different quantum wells have been calculated by using an iterative technique, which depends on experimentally obtained activation energy. Ground state energies also have been calculated with transfer matrix technique and compared with iteration results. Incorporating the effect of high electron density induced electron exchange interaction on ground state energies; more consistent results with theoretical transfer matrix calculations have been obtained.

Quantum Foundations of Quantum Information

NASA Astrophysics Data System (ADS)

Griffiths, Robert

2009-03-01

The main foundational issue for quantum information is: What is quantum information about? What does it refer to? Classical information typically refers to physical properties, and since classical is a subset of quantum information (assuming the world is quantum mechanical), quantum information should--and, it will be argued, does--refer to quantum physical properties represented by projectors on appropriate subspaces of a quantum Hilbert space. All sorts of microscopic and macroscopic properties, not just measurement outcomes, can be represented in this way, and are thus a proper subject of quantum information. The Stern-Gerlach experiment illustrates this. When properties are compatible, which is to say their projectors commute, Shannon's classical information theory based on statistical correlations extends without difficulty or change to the quantum case. When projectors do not commute, giving rise to characteristic quantum effects, a foundation for the subject can still be constructed by replacing the ``measurement and wave-function collapse'' found in textbooks--an efficient calculational tool, but one giving rise to numerous conceptual difficulties--with a fully consistent and paradox free stochastic formulation of standard quantum mechanics. This formulation is particularly helpful in that it contains no nonlocal superluminal influences; the reason the latter carry no information is that they do not exist.

Quantum mechanical calculations related to ionization and charge transfer in DNA

NASA Astrophysics Data System (ADS)

Cauët, E.; Valiev, M.; Weare, J. H.; Liévin, J.

2012-07-01

Ionization and charge migration in DNA play crucial roles in mechanisms of DNA damage caused by ionizing radiation, oxidizing agents and photo-irradiation. Therefore, an evaluation of the ionization properties of the DNA bases is central to the full interpretation and understanding of the elementary reactive processes that occur at the molecular level during the initial exposure and afterwards. Ab initio quantum mechanical (QM) methods have been successful in providing highly accurate evaluations of key parameters, such as ionization energies (IE) of DNA bases. Hence, in this study, we performed high-level QM calculations to characterize the molecular energy levels and potential energy surfaces, which shed light on ionization and charge migration between DNA bases. In particular, we examined the IEs of guanine, the most easily oxidized base, isolated and embedded in base clusters, and investigated the mechanism of charge migration over two and three stacked guanines. The IE of guanine in the human telomere sequence has also been evaluated. We report a simple molecular orbital analysis to explain how modifications in the base sequence are expected to change the efficiency of the sequence as a hole trap. Finally, the application of a hybrid approach combining quantum mechanics with molecular mechanics brings an interesting discussion as to how the native aqueous DNA environment affects the IE threshold of nucleobases.

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2.

PubMed

Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik; Harvey, Jeremy N; Mulholland, Adrian J

2016-06-20

The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site, but this is not a prerequisite for reaction via either mechanism. Several active site residues play a role in the binding of mexiletine in the active site, including Thr124 and Phe226. This work reveals key details of the N-hydroxylation of mexiletine and further demonstrates that mechanistic studies using QM/MM methods are useful for understanding drug metabolism.

Semiclassical description of hyperfine interaction in calculating chemically induced dynamic nuclear polarization in weak magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Purtov, P.A.; Salikhov, K.M.

1987-09-01

Semiclassical HFI description is applicable to calculating the integral CIDNP effect in weak fields. The HFI has been calculated for radicals with sufficiently numerous magnetically equivalent nuclei (n greater than or equal to 5) in satisfactory agreement with CIDNP calculations based on quantum-mechanical description of radical-pair spin dynamics.

Ortho-para H₂ conversion by proton exchange at low temperature: an accurate quantum mechanical study.

PubMed

Honvault, P; Jorfi, M; González-Lezana, T; Faure, A; Pagani, L

2011-07-08

We report extensive, accurate fully quantum, time-independent calculations of cross sections at low collision energies, and rate coefficients at low temperatures for the H⁺ + H₂(v = 0, j) → H⁺ + H₂(v = 0, j') reaction. Different transitions are considered, especially the ortho-para conversion (j = 1 → j' = 0) which is of key importance in astrophysics. This conversion process appears to be very efficient and dominant at low temperature, with a rate coefficient of 4.15 × 10⁻¹⁰ cm³ molecule⁻¹ s⁻¹ at 10 K. The quantum mechanical results are also compared with statistical quantum predictions and the reaction is found to be statistical in the low temperature regime (T < 100 K).

A comparative study of different methods for calculating electronic transition rates

NASA Astrophysics Data System (ADS)

Kananenka, Alexei A.; Sun, Xiang; Schubert, Alexander; Dunietz, Barry D.; Geva, Eitan

2018-03-01

We present a comprehensive comparison of the following mixed quantum-classical methods for calculating electronic transition rates: (1) nonequilibrium Fermi's golden rule, (2) mixed quantum-classical Liouville method, (3) mean-field (Ehrenfest) mixed quantum-classical method, and (4) fewest switches surface-hopping method (in diabatic and adiabatic representations). The comparison is performed on the Garg-Onuchic-Ambegaokar benchmark charge-transfer model, over a broad range of temperatures and electronic coupling strengths, with different nonequilibrium initial states, in the normal and inverted regimes. Under weak to moderate electronic coupling, the nonequilibrium Fermi's golden rule rates are found to be in good agreement with the rates obtained via the mixed quantum-classical Liouville method that coincides with the fully quantum-mechanically exact results for the model system under study. Our results suggest that the nonequilibrium Fermi's golden rule can serve as an inexpensive yet accurate alternative to Ehrenfest and the fewest switches surface-hopping methods.

Effects of Shannon entropy and electric field on polaron in RbCl triangular quantum dot

NASA Astrophysics Data System (ADS)

M, Tiotsop; A, J. Fotue; S, C. Kenfack; N, Issofa; H, Fotsin; L, C. Fai

2016-04-01

In this paper, the time evolution of the quantum mechanical state of a polaron is examined using the Pekar type variational method on the condition of the electric-LO-phonon strong-coupling and polar angle in RbCl triangular quantum dot. We obtain the eigenenergies, and the eigenfunctions of the ground state, and the first excited state respectively. This system in a quantum dot can be treated as a two-level quantum system qubit and the numerical calculations are performed. The effects of Shannon entropy and electric field on the polaron in the RbCl triangular quantum dot are also studied.

Spintronic characteristics of self-assembled neurotransmitter acetylcholine molecular complexes enable quantum information processing in neural networks and brain

NASA Astrophysics Data System (ADS)

Tamulis, Arvydas; Majauskaite, Kristina; Kairys, Visvaldas; Zborowski, Krzysztof; Adhikari, Kapil; Krisciukaitis, Sarunas

2016-09-01

Implementation of liquid state quantum information processing based on spatially localized electronic spin in the neurotransmitter stable acetylcholine (ACh) neutral molecular radical is discussed. Using DFT quantum calculations we proved that this molecule possesses stable localized electron spin, which may represent a qubit in quantum information processing. The necessary operating conditions for ACh molecule are formulated in self-assembled dimer and more complex systems. The main quantum mechanical research result of this paper is that the neurotransmitter ACh systems, which were proposed, include the use of quantum molecular spintronics arrays to control the neurotransmission in neural networks.

Hybrid plasmonic systems: from optical transparencies to strong coupling and entanglement

NASA Astrophysics Data System (ADS)

Gray, Stephen K.

2018-02-01

Classical electrodynamics and quantum mechanical models of quantum dots and molecules interacting with plasmonic systems are discussed. Calculations show that just one quantum dot interacting with a plasmonic system can lead to interesting optical effects, including optical transparencies and more general Fano resonance features that can be tailored with ultrafast laser pulses. Such effects can occur in the limit of moderate coupling between quantum dot and plasmonic system. The approach to the strong coupling regime is also discussed. In cases with two or more quantum dots within a plasmonic system, the possibility of quantum entanglement mediated through the dissipative plasmonic structure arises.

Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl- + CH3I Reaction in Water.

PubMed

Liu, Peng; Li, Chen; Wang, Dunyou

2017-10-19

The Cl - + CH 3 I → CH 3 Cl + I - reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.

Pentachlorophenol radical cations generated on Fe(III)-montmorillonite initiate octachlorodibenzo-p-dioxin formation in clays: DFT and FTIR studies

PubMed Central

Gu, Cheng; Liu, Cun; Johnston, Cliff T.; Teppen, Brian J.; Li, Hui; Boyd, Stephen A.

2011-01-01

Octachlorodibenzodioxin (OCDD) forms spontaneously from pentachlorophenol (PCP) on the surfaces of Fe(III)-saturated smectite clay (1). Here, we used in situ FTIR methods and quantum mechanical calculations to determine the mechanism by which this reaction is initiated. As the clay was dehydrated, vibrational spectra showed new peaks that grew and then reversibly disappeared as the clay rehydrated. First principle DFT calculations of hydrated Fe-PCP clusters reproduced these transient FTIR peaks when inner-sphere complexation and concomitant electron transfer produced Fe(II) and PCP radical cations. Thus, our experimental (FTIR) and theoretical (quantum mechanical) results mutually support the hypothesis that OCDD formation on Fe-smectite surfaces is initiated by the reversible formation of metastable PCP radical cations via single electron transfer from PCP to Fe(III). The negatively charged clay surface apparently selects for this reaction mechanism by stabilizing PCP radical cations. PMID:21254769

First principles calculation of thermo-mechanical properties of thoria using Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Malakkal, Linu; Szpunar, Barbara; Zuniga, Juan Carlos; Siripurapu, Ravi Kiran; Szpunar, Jerzy A.

2016-05-01

In this work, we have used Quantum ESPRESSO (QE), an open source first principles code, based on density-functional theory, plane waves, and pseudopotentials, along with quasi-harmonic approximation (QHA) to calculate the thermo-mechanical properties of thorium dioxide (ThO2). Using Python programming language, our group developed qe-nipy-advanced, an interface to QE, which can evaluate the structural and thermo-mechanical properties of materials. We predicted the phonon contribution to thermal conductivity (kL) using the Slack model. We performed the calculations within local density approximation (LDA) and generalized gradient approximation (GGA) with the recently proposed version for solids (PBEsol). We employed a Monkhorst-Pack 5 × 5 × 5 k-points mesh in reciprocal space with a plane wave cut-off energy of 150 Ry to obtain the convergence of the structure. We calculated the dynamical matrices of the lattice on a 4 × 4 × 4 mesh. We have predicted the heat capacity, thermal expansion and the phonon contribution to thermal conductivity, as a function of temperature up to 1400K, and compared them with the previous work and known experimental results.

Quantum kernel applications in medicinal chemistry.

PubMed

Huang, Lulu; Massa, Lou

2012-07-01

Progress in the quantum mechanics of biological molecules is being driven by computational advances. The notion of quantum kernels can be introduced to simplify the formalism of quantum mechanics, making it especially suitable for parallel computation of very large biological molecules. The essential idea is to mathematically break large biological molecules into smaller kernels that are calculationally tractable, and then to represent the full molecule by a summation over the kernels. The accuracy of the kernel energy method (KEM) is shown by systematic application to a great variety of molecular types found in biology. These include peptides, proteins, DNA and RNA. Examples are given that explore the KEM across a variety of chemical models, and to the outer limits of energy accuracy and molecular size. KEM represents an advance in quantum biology applicable to problems in medicine and drug design.

Quenching of para-H{sub 2} with an ultracold antihydrogen atom H{sub 1s}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sultanov, Renat A.; Guster, Dennis; Adhikari, Sadhan K.

2010-02-15

In this work we report the results of calculation for quantum-mechanical rotational transitions in molecular hydrogen, H{sub 2}, induced by an ultracold ground-state antihydrogen atom H{sub 1s}. The calculations are accomplished using a nonreactive close-coupling quantum-mechanical approach. The H{sub 2} molecule is treated as a rigid rotor. The total elastic-scattering cross section {sigma}{sub el}({epsilon}) at energy {epsilon}, state-resolved rotational transition cross sections {sigma}{sub jj}{sup '}({epsilon}) between states j and j{sup '}, and corresponding thermal rate coefficients k{sub jj}{sup '}(T) are computed in the temperature range 0.004 K < or approx. T < or approx. 4 K. Satisfactory agreement with othermore » calculations (variational) has been obtained for {sigma}{sub el}({epsilon}).« less

Quantum and quasi-classical collisional dynamics of O{sub 2}–Ar at high temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulusoy, Inga S.; Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400; Andrienko, Daniil A.

A hypersonic vehicle traveling at a high speed disrupts the distribution of internal states in the ambient flow and introduces a nonequilibrium distribution in the post-shock conditions. We investigate the vibrational relaxation in diatom-atom collisions in the range of temperatures between 1000 and 10 000 K by comparing results of extensive fully quantum-mechanical and quasi-classical simulations with available experimental data. The present paper simulates the interaction of molecular oxygen with argon as the first step in developing the aerothermodynamics models based on first principles. We devise a routine to standardize such calculations also for other scattering systems. Our results demonstrate verymore » good agreement of vibrational relaxation time, derived from quantum-mechanical calculations with the experimental measurements conducted in shock tube facilities. At the same time, the quasi-classical simulations fail to accurately predict rates of vibrationally inelastic transitions at temperatures lower than 3000 K. This observation and the computational cost of adopted methods suggest that the next generation of high fidelity thermochemical models should be a combination of quantum and quasi-classical approaches.« less

Quantum and quasi-classical collisional dynamics of O2-Ar at high temperatures

NASA Astrophysics Data System (ADS)

Ulusoy, Inga S.; Andrienko, Daniil A.; Boyd, Iain D.; Hernandez, Rigoberto

2016-06-01

A hypersonic vehicle traveling at a high speed disrupts the distribution of internal states in the ambient flow and introduces a nonequilibrium distribution in the post-shock conditions. We investigate the vibrational relaxation in diatom-atom collisions in the range of temperatures between 1000 and 10 000 K by comparing results of extensive fully quantum-mechanical and quasi-classical simulations with available experimental data. The present paper simulates the interaction of molecular oxygen with argon as the first step in developing the aerothermodynamics models based on first principles. We devise a routine to standardize such calculations also for other scattering systems. Our results demonstrate very good agreement of vibrational relaxation time, derived from quantum-mechanical calculations with the experimental measurements conducted in shock tube facilities. At the same time, the quasi-classical simulations fail to accurately predict rates of vibrationally inelastic transitions at temperatures lower than 3000 K. This observation and the computational cost of adopted methods suggest that the next generation of high fidelity thermochemical models should be a combination of quantum and quasi-classical approaches.

Combined multireference configuration interaction/ molecular dynamics approach for calculating solvatochromic shifts: application to the n(O) --> pi* electronic transition of formaldehyde.

PubMed

Xu, ZongRong; Matsika, Spiridoula

2006-11-02

A combined quantum mechanics/molecular mechanics method is described here for considering the solvatochromic shift of excited states in solution. The quantum mechanical solute is described using high level multireference configuration interaction methods (MRCI), while molecular dynamics is used for obtaining the structure of the solvent around the solute. The electrostatic effect of the solvent is included in the quantum description of the solute in an averaged way. This method is used to study solvent effects on the n(O) --> pi* electronic transition of formaldehyde in aqueous solution. The effects of solute polarization, basis sets, and dynamical correlation on the solvatochromic shift, and on dipole moments, have been investigated.

First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments.

PubMed

Roy, Tapta Kanchan; Sharma, Rahul; Gerber, R Benny

2016-01-21

First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data. Using hybrid HF/MP2 potentials, the Vibrational Self-Consistent Field with Second-Order Perturbation Correction (VSCF-PT2) algorithm is used to compute the spectra without any ad hoc scaling or fitting. All of the vibrational modes (135 for the largest system) are treated quantum mechanically and anharmonically using full pair-wise coupling potentials to represent the interaction between different modes. In the hybrid potential scheme the MP2 method is used for the harmonic part of the potential and a modified HF method is used for the anharmonic part. The overall agreement between computed spectra and experiment is very good and reveals different signatures for different conformers. This study shows that first-principles spectroscopic calculations of good accuracy are possible for dipeptides hence it opens possibilities for determination of dipeptide conformer structures by comparison of spectroscopic calculations with experiment.

Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations

NASA Astrophysics Data System (ADS)

Wong, Kin-Yiu

We have simulated two enzymatic reactions with molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) techniques. One reaction is the hydrolysis of the insecticide paraoxon catalyzed by phosphotriesterase (PTE). PTE is a bioremediation candidate for environments contaminated by toxic nerve gases (e.g., sarin) or pesticides. Based on the potential of mean force (PMF) and the structural changes of the active site during the catalysis, we propose a revised reaction mechanism for PTE. Another reaction is the hydrolysis of the second-messenger cyclic adenosine 3'-5'-monophosphate (cAMP) catalyzed by phosphodiesterase (PDE). Cyclicnucleotide PDE is a vital protein in signal-transduction pathways and thus a popular target for inhibition by drugs (e.g., ViagraRTM). A two-dimensional (2-D) free-energy profile has been generated showing that the catalysis by PDE proceeds in a two-step SN2-type mechanism. Furthermore, to characterize a chemical reaction mechanism in experiment, a direct probe is measuring kinetic isotope effects (KIEs). KIEs primarily arise from internuclear quantum-statistical effects, e.g., quantum tunneling and quantization of vibration. To systematically incorporate the quantum-statistical effects during MD simulations, we have developed an automated integration-free path-integral (AIF-PI) method based on Kleinert's variational perturbation theory for the centroid density of Feynman's path integral. Using this analytic method, we have performed ab initio pathintegral calculations to study the origin of KIEs on several series of proton-transfer reactions from carboxylic acids to aryl substituted alpha-methoxystyrenes in water. In addition, we also demonstrate that the AIF-PI method can be used to systematically compute the exact value of zero-point energy (beyond the harmonic approximation) by simply minimizing the centroid effective potential.

Comment on "Peres experiment using photons: No test for hypercomplex (quaternionic) quantum theories"

NASA Astrophysics Data System (ADS)

Procopio, Lorenzo M.; Rozema, Lee A.; Dakić, Borivoje; Walther, Philip

2017-09-01

In his recent article [Phys. Rev. A 95, 060101(R) (2017), 10.1103/PhysRevA.95.060101], Adler questions the usefulness of the bound found in our experimental search for genuine effects of hypercomplex quantum mechanics [Nat. Commun. 8, 15044 (2017), 10.1038/ncomms15044]. Our experiment was performed using a black-box (instrumentalist) approach to generalized probabilistic theories; therefore, it does not assume a priori any particular underlying mechanism. From that point of view our experimental results do indeed place meaningful bounds on the possible effects of "postquantum theories," including quaternionic quantum mechanics. In his article, Adler compares our experiment to nonrelativistic and Möller formal scattering theories within quaternionic quantum mechanics. With a particular set of assumptions, he finds that quaternionic effects would likely not manifest themselves in general. Although these assumptions are justified in the nonrelativistic case, a proper calculation for relativistic particles is still missing. Here, we provide a concrete relativistic example of Klein-Gordon scattering wherein the quaternionic effects persist. We note that when the Klein-Gordon equation is formulated using a Hamiltonian formalism it displays a so-called "indefinite metric," a characteristic feature of relativistic quantum wave equations. In Adler's example this is directly forbidden by his assumptions, and therefore our present example is not in contradiction to his work. In complex quantum mechanics this problem of an indefinite metric is solved in a second quantization. Unfortunately, there is no known algorithm for canonical field quantization in quaternionic quantum mechanics.

Optimum quantum receiver for detecting weak signals in PAM communication systems

NASA Astrophysics Data System (ADS)

Sharma, Navneet; Rawat, Tarun Kumar; Parthasarathy, Harish; Gautam, Kumar

2017-09-01

This paper deals with the modeling of an optimum quantum receiver for pulse amplitude modulator (PAM) communication systems. The information bearing sequence {I_k}_{k=0}^{N-1} is estimated using the maximum likelihood (ML) method. The ML method is based on quantum mechanical measurements of an observable X in the Hilbert space of the quantum system at discrete times, when the Hamiltonian of the system is perturbed by an operator obtained by modulating a potential V with a PAM signal derived from the information bearing sequence {I_k}_{k=0}^{N-1}. The measurement process at each time instant causes collapse of the system state to an observable eigenstate. All probabilities of getting different outcomes from an observable are calculated using the perturbed evolution operator combined with the collapse postulate. For given probability densities, calculation of the mean square error evaluates the performance of the receiver. Finally, we present an example involving estimating an information bearing sequence that modulates a quantum electromagnetic field incident on a quantum harmonic oscillator.

Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.

PubMed

Yilmazer, Nusret Duygu; Korth, Martin

2016-05-16

We review the first successes and failures of a "new wave" of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of "enhanced", dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

Reaction Mechanisms for the Electrochemical Reduction of CO2 to CO and Formate on the Cu(100) Surface at 298K from Quantum Mechanics Free Energy Calculations with Explicit Water.

PubMed

Cheng, Tao; Xiao, Hai; Goddard, William A

2016-10-11

Copper is the only elemental metal that reduces a significant fraction of CO 2 to hydrocarbons and alcohols, but the atomistic reaction mechanism that controls the product distributions are not known because it has not been possible to detect the reaction intermediates on the electrode surface experimentally, or carry out Quantum Mechanics (QM) calculations with a realistic description of the electrolyte (water). Here, we carry out Quantum Mechanics (QM) calculations with an explicit description of water on the Cu(100) surface (experimentally shown to be stable under CO2RR conditions) to examine the initial reaction pathways to form CO and formate (HCOO - ) from CO 2 through free energy calculations at 298K and pH 7. We find that CO formation proceeds from physisorbed CO 2 to chemisorbed CO 2 (*CO 2 δ- ), with a free energy barrier of ΔG ‡ =0.43 eV, the rate determining step (RDS). The subsequent barriers of protonating *CO 2 δ- to form COOH* and then dissociating COOH* to form *CO are 0.37 eV and 0.30 eV, respectively. HCOO - formation proceeds through a very different pathway in which physisorbed CO 2 reacts directly with a surface H* (along with electron transfer), leading to ΔG ‡ = 0.80 eV. Thus, the competition between CO formation and HCOO - formation occurs in the first electron transfer step. On Cu(100), the RDS for CO formation is lower, making CO the predominant product. Thus, to alter the product distribution we need to control this first step of CO 2 binding, which might involve alloying or changing the structure at the nanoscale.

Theoretical description of quantum mechanical permeation of graphene membranes by charged hydrogen isotopes

NASA Astrophysics Data System (ADS)

Mazzuca, James W.; Haut, Nathaniel K.

2018-06-01

It has been recently shown that in the presence of an applied voltage, hydrogen and deuterium nuclei can be separated from one another using graphene membranes as a nuclear sieve, resulting in a 10-fold enhancement in the concentration of the lighter isotope. While previous studies, both experimental and theoretical, have attributed this effect mostly to differences in vibrational zero point energy (ZPE) of the various isotopes near the membrane surface, we propose that multi-dimensional quantum mechanical tunneling of nuclei through the graphene membrane influences this proton permeation process in a fundamental way. We perform ring polymer molecular dynamics calculations in which we include both ZPE and tunneling effects of various hydrogen isotopes as they permeate the graphene membrane and compute rate constants across a range of temperatures near 300 K. While capturing the experimentally observed separation factor, our calculations indicate that the transverse motion of the various isotopes across the surface of the graphene membrane is an essential part of this sieving mechanism. An understanding of the multi-dimensional quantum mechanical nature of this process could serve to guide the design of other such isotopic enrichment processes for a variety of atomic and molecular species of interest.

Theoretical description of quantum mechanical permeation of graphene membranes by charged hydrogen isotopes.

PubMed

Mazzuca, James W; Haut, Nathaniel K

2018-06-14

It has been recently shown that in the presence of an applied voltage, hydrogen and deuterium nuclei can be separated from one another using graphene membranes as a nuclear sieve, resulting in a 10-fold enhancement in the concentration of the lighter isotope. While previous studies, both experimental and theoretical, have attributed this effect mostly to differences in vibrational zero point energy (ZPE) of the various isotopes near the membrane surface, we propose that multi-dimensional quantum mechanical tunneling of nuclei through the graphene membrane influences this proton permeation process in a fundamental way. We perform ring polymer molecular dynamics calculations in which we include both ZPE and tunneling effects of various hydrogen isotopes as they permeate the graphene membrane and compute rate constants across a range of temperatures near 300 K. While capturing the experimentally observed separation factor, our calculations indicate that the transverse motion of the various isotopes across the surface of the graphene membrane is an essential part of this sieving mechanism. An understanding of the multi-dimensional quantum mechanical nature of this process could serve to guide the design of other such isotopic enrichment processes for a variety of atomic and molecular species of interest.

Combined spectroscopic, molecular docking and quantum mechanics study of β-casein and p-coumaric acid interactions following thermal treatment.

PubMed

Kaur, Jasmeet; Katopo, Lita; Hung, Andrew; Ashton, John; Kasapis, Stefan

2018-06-30

The molecular nature of interactions between β-casein and p-coumaric acid was studied following exposure of their solutions to ultra-high temperature (UHT at 145 °C). Interactions were characterised by employing multi-spectroscopic methods, molecular docking and quantum mechanics calculations. FTIR demonstrates that the ligand lies in the vicinity of the protein, hence inverting the absorbance spectrum of the complex. This outcome changes the conformational characteristics of the protein leading to a flexible and open structure that accommodates the phenolic microconstituent. Results are supported by UV-vis, CD and fluorescence quenching showing considerable shifts in spectra with complexation. Molecular docking indicates that there is at least a hydrogen bond between p-coumaric acid and the peptide backbone of isoleucine (Ile27). Quantum mechanics calculations further argue that changes in experimental observations are also due to a covalent interaction in the protein-phenolic adduct, which according to the best predicted binding pose involves the side chain of lysine 47. Copyright © 2018. Published by Elsevier Ltd.

Effects of strain and quantum confinement in optically pumped nuclear magnetic resonance in GaAs: Interpretation guided by spin-dependent band structure calculations

DOE PAGES

Wood, R. M.; Saha, D.; McCarthy, L. A.; ...

2014-10-29

A combined experimental-theoretical study of optically pumped NMR (OPNMR) has been performed in a GaAs/Al 0.1Ga 0.9As quantum well film with thermally induced biaxial strain. The photon energy dependence of the Ga-71 OPNMR signal was recorded at magnetic fields of 4.9 and 9.4 T at a temperature of 4.8-5.4 K. The data were compared to the nuclear spin polarization calculated from differential absorption to spin-up and spin-down states of the conduction band using a modified Pidgeon Brown model. Reasonable agreement between theory and experiment is obtained, facilitating assignment of features in the OPNMR energy dependence to specific interband transitions. Despitemore » the approximations made in the quantum-mechanical model and the inexact correspondence between the experimental and calculated observables, the results provide insight into how effects of strain and quantum confinement are manifested in OPNMR signals« less

Electronic-topological study of the structure-activity relationships in a series of steroids with mineralocorticoid binding affinity.

PubMed

Kandemirli, Fatma; Tokay, Nesrin; Shvets, Nataly M; Dimoglo, Anatoly S

2003-01-01

Conformational analysis and quantum chemical calculations were carried out using molecular mechanics (MMP2) and semi-empirical quantum chemistry (CNDO/2) methods for 51 steroid homologues belonging to a series of 17-spirolactones. Matrices called Electronic-Topological Matrices of Conjunction (ETMCs) were formed using data obtained from quantum chemical calculations. A structural fragment of activity was identified in the series of steroids. As seen from the fragment's properties, active compounds are characterized by the presence of two atoms of oxygen, O1 and O3, which are situated at a distance of 13.5 A and possess high negative charges (-0.29 to -0.31 e).

Controlling the thermoelectric effect by mechanical manipulation of the electron's quantum phase in atomic junctions.

PubMed

Aiba, Akira; Demir, Firuz; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Tsukagoshi, Kazuhito; Saffarzadeh, Alireza; Kirczenow, George; Kiguchi, Manabu

2017-08-11

The thermoelectric voltage developed across an atomic metal junction (i.e., a nanostructure in which one or a few atoms connect two metal electrodes) in response to a temperature difference between the electrodes, results from the quantum interference of electrons that pass through the junction multiple times after being scattered by the surrounding defects. Here we report successfully tuning this quantum interference and thus controlling the magnitude and sign of the thermoelectric voltage by applying a mechanical force that deforms the junction. The observed switching of the thermoelectric voltage is reversible and can be cycled many times. Our ab initio and semi-empirical calculations elucidate the detailed mechanism by which the quantum interference is tuned. We show that the applied strain alters the quantum phases of electrons passing through the narrowest part of the junction and hence modifies the electronic quantum interference in the device. Tuning the quantum interference causes the energies of electronic transport resonances to shift, which affects the thermoelectric voltage. These experimental and theoretical studies reveal that Au atomic junctions can be made to exhibit both positive and negative thermoelectric voltages on demand, and demonstrate the importance and tunability of the quantum interference effect in the atomic-scale metal nanostructures.

Indication for quantum Darwinism in electron billiards

NASA Astrophysics Data System (ADS)

Brunner, R.; Akis, R.; Meisels, R.; Kuchar, F.; Ferry, D. K.

2010-02-01

In this paper, we investigate the dynamics in electron billiards by using classical and quantum mechanical calculations. We report on the existence of pointer states in single-dot and double-dot electron billiards. Additionally, we show that the two types of pointer states have the propensity to create offspring, i.e. they can be observed in the individual modes propagating between the external reservoirs. This can be understood as an indication that quantum Darwinism is present in the electron billiards.

Ab Initio Potential Energy Surfaces and Quantum Dynamics for Polyatomic Bimolecular Reactions.

PubMed

Fu, Bina; Zhang, Dong H

2018-05-08

There has been great progress in the development of potential energy surfaces (PESs) and quantum dynamics calculations in the gas phase. The establishment of a fitting procedure for highly accurate PESs and new developments in quantum reactive scattering on reliable PESs allow accurate characterization of reaction dynamics beyond triatomic systems. This review will give the recent development in our group in constructing ab initio PESs based on neural networks and the time-dependent wave packet calculations for bimolecular reactions beyond three atoms. Bimolecular reactions of current interest to the community, namely, OH + H 2 , H + H 2 O, OH + CO, H + CH 4 , and Cl + CH 4 , are focused on. Quantum mechanical characterization of these reactions uncovers interesting dynamical phenomena with an unprecedented level of sophistication and has greatly advanced our understanding of polyatomic reaction dynamics.

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

ERIC Educational Resources Information Center

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

2015-01-01

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

Frequency-domain multiscale quantum mechanics/electromagnetics simulation method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Lingyi; Yin, Zhenyu; Yam, ChiYung, E-mail: yamcy@yangtze.hku.hk, E-mail: ghc@everest.hku.hk

A frequency-domain quantum mechanics and electromagnetics (QM/EM) method is developed. Compared with the time-domain QM/EM method [Meng et al., J. Chem. Theory Comput. 8, 1190–1199 (2012)], the newly developed frequency-domain QM/EM method could effectively capture the dynamic properties of electronic devices over a broader range of operating frequencies. The system is divided into QM and EM regions and solved in a self-consistent manner via updating the boundary conditions at the QM and EM interface. The calculated potential distributions and current densities at the interface are taken as the boundary conditions for the QM and EM calculations, respectively, which facilitate themore » information exchange between the QM and EM calculations and ensure that the potential, charge, and current distributions are continuous across the QM/EM interface. Via Fourier transformation, the dynamic admittance calculated from the time-domain and frequency-domain QM/EM methods is compared for a carbon nanotube based molecular device.« less

Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling.

PubMed

Dzierlenga, Michael W; Antoniou, Dimitri; Schwartz, Steven D

2015-04-02

The mechanisms involved in enzymatic hydride transfer have been studied for years, but questions remain due, in part, to the difficulty of probing the effects of protein motion and hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and human heart lactate dehydrogenase (LDH). Calculation of the work applied to the hydride allowed for observation of the change in barrier height upon inclusion of quantum dynamics. Similar calculations were performed using deuterium as the transferring particle in order to approximate kinetic isotope effects (KIEs). The change in barrier height in YADH is indicative of a zero-point energy (ZPE) contribution and is evidence that catalysis occurs via a protein compression that mediates a near-barrierless hydride transfer. Calculation of the KIE using the difference in barrier height between the hydride and deuteride agreed well with experimental results.

Quantum Tunneling in Testosterone 6β-Hydroxylation by Cytochrome P450: Reaction Dynamics Calculations Employing Multiconfiguration Molecular-Mechanical Potential Energy Surfaces

NASA Astrophysics Data System (ADS)

Zhang, Yan; Lin, Hai

2009-05-01

Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

Interactions between Ground State Oxygen Atoms and Molecules: O - O and O (sub2) - O (sub2)

NASA Technical Reports Server (NTRS)

Vanderslice, Joseph T.; Mason, Edward A.; Maisch, William G.

1960-01-01

Potential energy curves for O - O interactions corresponding to the X (sup 3) Sigma - g, 1 delta g, 1 Sigma plus g, 3 delta u, A3 Sigma plus u, 1 Sigma - u, and B3 Sigma states of O (sub 2) have been calculated from spectroscopic data by the Rydberg-Klein-Rees method. Curves for the remaining twelve states of O (sub 2) dissociating to ground state atoms have been obtained from relations derived from approximate quantum-mechanical calculations, and checked against the meager experimental information available. Two semi-independent calculations have been made, and are in good agreement with each other. The quantum-mechanical relations also lead to an approximate O (sub 2) - O (sub 2) interaction, which is consistent with interactions derived from vibrational relaxation times and from high-temperature gas viscosity data.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Hybrid Quantum Mechanical/Molecular Mechanics Study of the SN2 Reaction of CH3Cl+OH- in Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Hongyun; Wang, Dunyou; Valiev, Marat

2011-11-03

The SN2 mechanism for the reaction of CH3Cl + OH- in aqueous solution was investigated using combined quantum mechanical and molecular mechanics methodology. We analyzed structures of reactant, transition and product states along the reaction pathway. The free energy profile was calculated using the multi-layered representation with the DFT and CCSD(T) level of theory for the quantum-mechanical description of the reactive region. Our results show that the aqueous environment has a significant impact on the reaction process. We find that solvation energy contribution raises the reaction barrier by ~18.9 kcal/mol and the reaction free energy by ~24.5 kcal/mol. The presencemore » of the solvent also induces perturbations in the electronic structure of the solute leading to an increase of 3.5 kcal/mol for the reaction barrier and a decrease of 5.6 kcal/mol for the reaction free energy respectively. Combining the results of two previous calculation results on CHCl3 + OH- and CH2Cl2 + OH- reactions in water, we demonstrate that increase in the chlorination of the methyl group (from CH3Cl to CHCl3) is accompanied by the decrease in the free energy reaction barrier, with the CH3Cl + OH- having the largest barrier among the three reactions.« less

Quantum chemical determination of Young's modulus of lignin. Calculations on a beta-O-4' model compound.

PubMed

Elder, Thomas

2007-11-01

The calculation of Young's modulus of lignin has been examined by subjecting a dimeric model compound to strain, coupled with the determination of energy and stress. The computational results, derived from quantum chemical calculations, are in agreement with available experimental results. Changes in geometry indicate that modifications in dihedral angles occur in response to linear strain. At larger levels of strain, bond rupture is evidenced by abrupt changes in energy, structure, and charge. Based on the current calculations, the bond scission may be occurring through a homolytic reaction between aliphatic carbon atoms. These results may have implications in the reactivity of lignin especially when subjected to processing methods that place large mechanical forces on the structure.

Matrix elements of explicitly correlated Gaussian basis functions with arbitrary angular momentum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joyce, Tennesse; Varga, Kálmán

2016-05-14

A new algorithm for calculating the Hamiltonian matrix elements with all-electron explicitly correlated Gaussian functions for quantum-mechanical calculations of atoms with arbitrary angular momentum is presented. The calculations are checked on several excited states of three and four electron systems. The presented formalism can be used as unified framework for high accuracy calculations of properties of small atoms and molecules.

Quantum mechanism of nonlocal Gilbert damping in magnetic trilayers

NASA Astrophysics Data System (ADS)

Barati, Ehsan; Cinal, Marek

2015-06-01

A fully quantum-mechanical calculation of the Gilbert damping constant α in magnetic trilayers is done by employing the torque-correlation formula within a realistic tight-binding model. A remarkable enhancement of α in Co/NM1/NM2 trilayers is obtained due to adding the caps NM2=Pd, Pt, and it decays with the thickness of the spacers NM1=Cu, Ag, Au in agreement with experiment. Nonlocal origin of the Gilbert damping is visualized with its atomic layer contributions. It is shown that magnetization in Co is damped remotely by strong spin-orbit coupling in NM2 via quantum states with large amplitude in both Co and NM2.

Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms.

PubMed

Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

2018-05-30

Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

PubMed

Faheem, Muhammad; Heyden, Andreas

2014-08-12

We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

Theoretical Modeling of Hydrogen Bonding in omolecular Solutions: The Combination of Quantum Mechanics and Molecular Mechanics

NASA Astrophysics Data System (ADS)

Ma, Jing; Jiang, Nan; Li, Hui

Hydrogen bonding interaction takes an important position in solutions. The non-classic nature of hydrogen bonding requires the resource-demanding quantum mechanical (QM) calculations. The molecular mechanics (MM) method, with much lower computational load, is applicable to the large-sized system. The combination of QM and MM is an efficient way in the treatment of solution. Taking advantage of the low-cost energy-based fragmentation QM approach (in which the o-molecule is divided into several subsystems, and QM calculation is carried out on each subsystem that is embedded in the environment of background charges of distant parts), the fragmentation-based QM/MM and polarization models have been implemented for the modeling of o-molecule in aqueous solutions, respectively. Within the framework of the fragmentation-based QM/MM hybrid model, the solute is treated by the fragmentation QM calculation while the numerous solvent molecules are described by MM. In the polarization model, the polarizability is considered by allowing the partial charges and fragment-centered dipole moments to be variables, with values coming from the energy-based fragmentation QM calculations. Applications of these two methods to the solvated long oligomers and cyclic peptides have demonstrated that the hydrogen bonding interaction affects the dynamic change in chain conformations of backbone.

Strain-enhanced tunneling magnetoresistance in MgO magnetic tunnel junctions

PubMed Central

Loong, Li Ming; Qiu, Xuepeng; Neo, Zhi Peng; Deorani, Praveen; Wu, Yang; Bhatia, Charanjit S.; Saeys, Mark; Yang, Hyunsoo

2014-01-01

While the effects of lattice mismatch-induced strain, mechanical strain, as well as the intrinsic strain of thin films are sometimes detrimental, resulting in mechanical deformation and failure, strain can also be usefully harnessed for applications such as data storage, transistors, solar cells, and strain gauges, among other things. Here, we demonstrate that quantum transport across magnetic tunnel junctions (MTJs) can be significantly affected by the introduction of controllable mechanical strain, achieving an enhancement factor of ~2 in the experimental tunneling magnetoresistance (TMR) ratio. We further correlate this strain-enhanced TMR with coherent spin tunneling through the MgO barrier. Moreover, the strain-enhanced TMR is analyzed using non-equilibrium Green's function (NEGF) quantum transport calculations. Our results help elucidate the TMR mechanism at the atomic level and can provide a new way to enhance, as well as tune, the quantum properties in nanoscale materials and devices. PMID:25266219

Comparison of cross sections from the quasi-classical trajectory method and the j(z)-conserving centrifugal sudden approximation with accurate quantum results for an atom-rigid nonlinear polyatomic collision

NASA Technical Reports Server (NTRS)

Schwenke, David W.

1993-01-01

We report the results of a series of calculations of state-to-state integral cross sections for collisions between O and nonvibrating H2O in the gas phase on a model nonreactive potential energy surface. The dynamical methods used include converged quantum mechanical scattering calculations, the j(z) conserving centrifugal sudden (j(z)-CCS) approximation, and quasi-classical trajectory (QCT) calculations. We consider three total energies 0.001, 0.002, and 0.005 E(h) and the nine initial states with rotational angular momentum less than or equal to 2 (h/2 pi). The j(z)-CCS approximation gives good results, while the QCT method can be quite unreliable for transitions to specific rotational sublevels. However, the QCT cross sections summed over final sublevels and averaged over initial sublevels are in better agreement with the quantum results.

Signatures of Förster and Dexter transfer processes in coupled nanostructures for linear and two-dimensional coherent optical spectroscopy

NASA Astrophysics Data System (ADS)

Specht, Judith F.; Richter, Marten

2015-03-01

In this manuscript, we study the impact of the two Coulomb induced resonance energy transfer processes, Förster and Dexter coupling, on the spectral signatures obtained by double quantum coherence spectroscopy. We show that the specific coupling characteristics allow us to identify the underlying excitation transfer mechanism by means of specific signatures in coherent spectroscopy. Therefore, we control the microscopic calculated coupling strength of spin preserving and spin flipping Förster transfer processes by varying the mutual orientation of the two quantum emitters. The calculated spectra reveal the optical selection rules altered by Förster and Dexter coupling between two semiconductor quantum dots. We show that Dexter coupling between bright and dark two-exciton states occurs.

H{sub 2} dissociation due to collisions with He

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohlinger, L.; Forrey, R. C.; Lee, Teck-Ghee

2007-10-15

Cross sections for dissociation of H{sub 2} due to collision with He are calculated for highly excited rovibrational states using the quantum-mechanical coupled-states approximation. An L{sup 2} Sturmian basis set with multiple length scales is used to provide a discrete representation of the H{sub 2} continuum which includes orbiting resonances and a nonresonant background. Cross sections are given over a range of translational energies for both resonant and nonresonant dissociation together with the most important bound-state transitions for many different initial states. The results demonstrate that it is possible to compute converged quantum-mechanical cross sections using basis sets of modestmore » size. It is found that collision-induced dissociation competes with inelastic scattering as a depopulation mechanism for the highly excited states. The relevance of the present calculations to astrophysical models is discussed.« less

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots.

PubMed

Kazemi, Masoud; Åqvist, Johan

2015-06-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies.

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

PubMed Central

Kazemi, Masoud; Åqvist, Johan

2015-01-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies. PMID:26028237

Investigation of trypsin-CdSe quantum dot interactions via spectroscopic methods and effects on enzymatic activity.

PubMed

Kaur, Gurvir; Tripathi, S K

2015-01-05

The paper presents the interactions between trypsin and water soluble cadmium selenide (CdSe) quantum dots investigated by spectrophotometric methods. CdSe quantum dots have strong ability to quench the intrinsic fluorescence of trypsin by a static quenching mechanism. The quenching has been studied at three different temperatures where the results revealed that electrostatic interactions exist between CdSe quantum dots and trypsin and are responsible to stabilize the complex. The Scatchard plot from quenching revealed 1 binding site for quantum dots by trypsin, the same has been confirmed by making isothermal titrations of quantum dots against trypsin. The distance between donor and acceptor for trypsin-CdSe quantum dot complexes is calculated to be 2.8 nm by energy transfer mechanisms. The intrinsic fluorescence of CdSe quantum dots has also been enhanced by the trypsin, and is linear for concentration of trypsin ranging 1-80 μl. All the observations evidence the formation of trypsin-CdSe quantum dot conjugates, where trypsin retains the enzymatic activity which in turn is temperature and pH dependent. Copyright © 2014 Elsevier B.V. All rights reserved.

Perturbatively deformed defects in Pöschl-Teller-driven scenarios for quantum mechanics

NASA Astrophysics Data System (ADS)

Bernardini, Alex E.; da Rocha, Roldão

2016-07-01

Pöschl-Teller-driven solutions for quantum mechanical fluctuations are triggered off by single scalar field theories obtained through a systematic perturbative procedure for generating deformed defects. The analytical properties concerning the quantum fluctuations in one-dimension, zero-mode states, first- and second-excited states, and energy density profiles are all obtained from deformed topological and non-topological structures supported by real scalar fields. Results are firstly derived from an integrated λϕ4 theory, with corresponding generalizations applied to starting λχ4 and sine-Gordon theories. By focusing our calculations on structures supported by the λϕ4 theory, the outcome of our study suggests an exact quantitative correspondence to Pöschl-Teller-driven systems. Embedded into the perturbative quantum mechanics framework, such a correspondence turns into a helpful tool for computing excited states and continuous mode solutions, as well as their associated energy spectrum, for quantum fluctuations of perturbatively deformed structures. Perturbative deformations create distinct physical scenarios in the context of exactly solvable quantum systems and may also work as an analytical support for describing novel braneworld universes embedded into a 5-dimensional gravity bulk.

[Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

PubMed

Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I

2013-01-01

To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

Low-Dimensional Nanostructures and a Semiclassical Approach for Teaching Feynman's Sum-over-Paths Quantum Theory

ERIC Educational Resources Information Center

Onorato, P.

2011-01-01

An introduction to quantum mechanics based on the sum-over-paths (SOP) method originated by Richard P. Feynman and developed by E. F. Taylor and coworkers is presented. The Einstein-Brillouin-Keller (EBK) semiclassical quantization rules are obtained following the SOP approach for bounded systems, and a general approach to the calculation of…

Quantum mechanics over sets

NASA Astrophysics Data System (ADS)

Ellerman, David

2014-03-01

In models of QM over finite fields (e.g., Schumacher's ``modal quantum theory'' MQT), one finite field stands out, Z2, since Z2 vectors represent sets. QM (finite-dimensional) mathematics can be transported to sets resulting in quantum mechanics over sets or QM/sets. This gives a full probability calculus (unlike MQT with only zero-one modalities) that leads to a fulsome theory of QM/sets including ``logical'' models of the double-slit experiment, Bell's Theorem, QIT, and QC. In QC over Z2 (where gates are non-singular matrices as in MQT), a simple quantum algorithm (one gate plus one function evaluation) solves the Parity SAT problem (finding the parity of the sum of all values of an n-ary Boolean function). Classically, the Parity SAT problem requires 2n function evaluations in contrast to the one function evaluation required in the quantum algorithm. This is quantum speedup but with all the calculations over Z2 just like classical computing. This shows definitively that the source of quantum speedup is not in the greater power of computing over the complex numbers, and confirms the idea that the source is in superposition.

Path Integrals for Electronic Densities, Reactivity Indices, and Localization Functions in Quantum Systems

PubMed Central

Putz, Mihai V.

2009-01-01

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr’s quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions – all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems. PMID:20087467

Path integrals for electronic densities, reactivity indices, and localization functions in quantum systems.

PubMed

Putz, Mihai V

2009-11-10

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr's quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions - all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems.

Study of quantum confinement effects in ZnO nanostructures

NASA Astrophysics Data System (ADS)

Movlarooy, Tayebeh

2018-03-01

Motivation to fact that zinc oxide nanowires and nanotubes with successful synthesis and the mechanism of formation, stability and electronic properties have been investigated; in this study the structural, electronic properties and quantum confinement effects of zinc oxide nanotubes and nanowires with different diameters are discussed. The calculations within density functional theory and the pseudo potential approximation are done. The electronic structure and energy gap for Armchair and zigzag ZnO nanotubes with a diameter of about 4 to 55 Angstrom and ZnO nanowires with a diameter range of 4 to 23 Å is calculated. The results revealed that due to the quantum confinement effects, by reducing the diameter of nanowires and nanotubes, the energy gap increases. Zinc oxide semiconductor nanostructures since having direct band gap with size-dependent and quantum confinement effect are recommended as an appropriate candidate for making nanoscale optoelectronic devices.

Multiscale Modeling of Fracture in an SiO2 Nanorod

NASA Astrophysics Data System (ADS)

Mallik, Aditi

2005-11-01

The fracture of a 108 particle SiO2 nanorod under uniaxial strain is described using an NDDO quantum mechanics. The stress -- strain curve to failure is calculated as a function of strain rate to show a domain that is independent of strain rate. A pair potential for use in classical MD is constructed such that the elastic portion of the quantum curve is reproduced. However, it is shown that the classical analysis does not describe accurately the large strain behavior and failure. Finally, a composite rod is constructed with a small subsystem described by quantum mechanics and the remainder described by classical MD ^1. The stress -- strain curves for the classical, quantum, and composite rods are compared and contrasted. 1. ``Multiscale Modeling of Materials -- Concepts and Illustration'', A. Mallik, K. Runge, J. Dufty, and H-P Cheng, cond-mat 0507558.

REVIEWS OF TOPICAL PROBLEMS: Analytic calculations on digital computers for applications in physics and mathematics

NASA Astrophysics Data System (ADS)

Gerdt, V. P.; Tarasov, O. V.; Shirkov, Dmitrii V.

1980-01-01

The present state of analytic calculations on computers is reviewed. Several programming systems which are used for analytic calculations are discussed: SCHOONSCHIP, CLAM, REDUCE-2, SYMBAL, CAMAL, AVTO-ANALITIK, MACSYMA, etc. It is shown that these systems can be used to solve a wide range of problems in physics and mathematics. Some physical applications are discussed in celestial mechanics, the general theory of relativity, quantum field theory, plasma physics, hydrodynamics, atomic and molecular physics, and quantum chemistry. Some mathematical applications which are discussed are evaluating indefinite integrals, solving differential equations, and analyzing mathematical expressions. This review is addressed to physicists and mathematicians working in a wide range of fields.

Real-Time Quantum Dynamics of Long-Range Electronic Excitation Transfer in Plasmonic Nanoantennas.

PubMed

Ilawe, Niranjan V; Oviedo, M Belén; Wong, Bryan M

2017-08-08

Using large-scale, real-time, quantum dynamics calculations, we present a detailed analysis of electronic excitation transfer (EET) mechanisms in a multiparticle plasmonic nanoantenna system. Specifically, we utilize real-time, time-dependent, density functional tight binding (RT-TDDFTB) to provide a quantum-mechanical description (at an electronic/atomistic level of detail) for characterizing and analyzing these systems, without recourse to classical approximations. We also demonstrate highly long-range electronic couplings in these complex systems and find that the range of these couplings is more than twice the conventional cutoff limit considered by Förster resonance energy transfer (FRET)-based approaches. Furthermore, we attribute these unusually long-ranged electronic couplings to the coherent oscillations of conduction electrons in plasmonic nanoparticles. This long-range nature of plasmonic interactions has important ramifications for EET; in particular, we show that the commonly used "nearest-neighbor" FRET model is inadequate for accurately characterizing EET even in simple plasmonic antenna systems. These findings provide a real-time, quantum-mechanical perspective for understanding EET mechanisms and provide guidance in enhancing plasmonic properties in artificial light-harvesting systems.

Quantum mechanical tunneling in the automerization of cyclobutadiene

NASA Astrophysics Data System (ADS)

Schoonmaker, R.; Lancaster, T.; Clark, S. J.

2018-03-01

Cyclobutadiene has a four-membered carbon ring with two double bonds, but this highly strained molecular configuration is almost square and, via a coordinated motion, the nuclei quantum mechanically tunnels through the high-energy square state to a configuration equivalent to the initial configuration under a 90° rotation. This results in a square ground state, comprising a superposition of two molecular configurations, that is driven by quantum tunneling. Using a quantum mechanical model, and an effective nuclear potential from density functional theory, we calculate the vibrational energy spectrum and the accompanying wavefunctions. We use the wavefunctions to identify the motions of the molecule and detail how different motions can enhance or suppress the tunneling rate. This is relevant for kinematics of tunneling-driven reactions, and we discuss these implications. We are also able to provide a qualitative account of how the molecule will respond to an external perturbation and how this may enhance or suppress infra-red-active vibrational transitions.

Conformal quantum mechanics and holography in noncommutative space-time

NASA Astrophysics Data System (ADS)

Gupta, Kumar S.; Harikumar, E.; Zuhair, N. S.

2017-09-01

We analyze the effects of noncommutativity in conformal quantum mechanics (CQM) using the κ-deformed space-time as a prototype. Up to the first order in the deformation parameter, the symmetry structure of the CQM algebra is preserved but the coupling in a canonical model of the CQM gets deformed. We show that the boundary conditions that ensure a unitary time evolution in the noncommutative CQM can break the scale invariance, leading to a quantum mechanical scaling anomaly. We calculate the scaling dimensions of the two and three point functions in the noncommutative CQM which are shown to be deformed. The AdS2 / CFT1 duality for the CQM suggests that the corresponding correlation functions in the holographic duals are modified. In addition, the Breitenlohner-Freedman bound also picks up a noncommutative correction. The strongly attractive regime of a canonical model of the CQM exhibit quantum instability. We show that the noncommutativity softens this singular behaviour and its implications for the corresponding holographic duals are discussed.

Quantitative Hydrocarbon Energies from the PMO Method.

ERIC Educational Resources Information Center

Cooper, Charles F.

1979-01-01

Details a procedure for accurately calculating the quantum mechanical energies of hydrocarbons using the perturbational molecular orbital (PMO) method, which does not require the use of a computer. (BT)

QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations.

PubMed

Dyekjaer, Jane Dannow; Jónsdóttir, Svava Osk

2004-01-22

Quantitative Structure-Property Relationships (QSPR) have been developed for a series of monosaccharides, including the physical properties of partial molar heat capacity, heat of solution, melting point, heat of fusion, glass-transition temperature, and solid state density. The models were based on molecular descriptors obtained from molecular mechanics and quantum chemical calculations, combined with other types of descriptors. Saccharides exhibit a large degree of conformational flexibility, therefore a methodology for selecting the energetically most favorable conformers has been developed, and was used for the development of the QSPR models. In most cases good correlations were obtained for monosaccharides. For five of the properties predictions were made for disaccharides, and the predicted values for the partial molar heat capacities were in excellent agreement with experimental values.

Magnetic-field-mediated coupling and control in hybrid atomic-nanomechanical systems

NASA Astrophysics Data System (ADS)

Tretiakov, A.; LeBlanc, L. J.

2016-10-01

Magnetically coupled hybrid quantum systems enable robust quantum state control through Landau-Zener transitions. Here, we show that an ultracold atomic sample magnetically coupled to a nanomechanical resonator can be used to cool the resonator's mechanical motion, to measure the mechanical temperature, and to enable entanglement of more than one of these mesoscopic objects. We calculate the expected coupling for both permanent-magnet and current-conducting nanostring resonators and describe how this hybridization is attainable using recently developed fabrication techniques, including SiN nanostrings and atom chips.

Ionization of deep quantum wells: Optical trampoline effect

NASA Astrophysics Data System (ADS)

Perlin, E. Yu.; Levitskiĭ, R. S.

2007-02-01

A new mechanism of transitions of an electronic system from the ground state to states with excitation energies exceeding many times the energy of a light photon initiating the transitions has been considered. This mechanism is based on the so-called optical “trampoline” effect: one of the interacting electrons receives energy from another electron and, simultaneously absorbing a photon ħω, overcomes the energy gap significantly exceeding ħω. Ionization of deep quantum wells by low-frequency light of moderate intensity due to the optical trampoline effect was calculated.

Fully differential cross sections for the single ionization of helium by fast ions: Classical model calculations

NASA Astrophysics Data System (ADS)

Sarkadi, L.

2018-04-01

Fully differential cross sections (FDCSs) have been calculated for the single ionization of helium by 1- and 3-MeV proton and 100-MeV/u C6 + ion impact using the classical trajectory Monte Carlo (CTMC) method in the nonrelativistic, three-body approximation. The calculations were made employing a Wigner-type model in which the quantum-mechanical position distribution of the electron is approximated by a weighted integral of the microcanonical distribution over a range of the binding energy of the electron. In the scattering plane, the model satisfactorily reproduces the observed shape of the binary peak. In the region of the peak the calculated FDCSs agree well with the results of continuum-distorted-wave calculations for all the investigated collisions. For 1-MeV proton impact the experimentally observed shift of the binary peak with respect to the first Born approximation is compared with the shifts obtained by different higher-order quantum-mechanical theories and the present CTMC method. The best result was achieved by CTMC, but still a large part of the shift remained unexplained. Furthermore, it was found that the classical theory failed to reproduce the shape of the recoil peak observed in the experiments, it predicts a much narrower peak. This indicates that the formation of the recoil peak is dominated by quantum-mechanical effects. For 100-MeV/u C6 + ion impact the present CTMC calculations confirmed the existence of the "double-peak" structure of the angular distribution of the electron in the plane perpendicular to the momentum transfer, in accordance with the observation, the prediction of an incoherent semiclassical model, and previous CTMC results. This finding together with wave-packet calculations suggests that the "C6 + puzzle" may be solved by considering the loss of the projectile coherence. Experiments to be conducted using ion beams of anisotropic coherence are proposed for a more differential investigation of the ionization dynamics.

On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study

NASA Astrophysics Data System (ADS)

Daidone, Isabella; Amadei, Andrea; Aschi, Massimiliano; Zanetti-Polzi, Laura

2018-03-01

We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.

Quantum treatment of protons with the reduced explicitly correlated Hartree-Fock approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirjoosingh, Andrew; Pak, Michael V.; Brorsen, Kurt R.

2015-06-07

The nuclear-electronic orbital (NEO) approach treats select nuclei quantum mechanically on the same level as the electrons and includes nonadiabatic effects between the electrons and the quantum nuclei. The practical implementation of this approach is challenging due to the significance of electron-nucleus dynamical correlation. Herein, we present a general extension of the previously developed reduced NEO explicitly correlated Hartree-Fock (RXCHF) approach, in which only select electronic orbitals are explicitly correlated to each quantum nuclear orbital via Gaussian-type geminal functions. Approximations of the electronic exchange between the geminal-coupled electronic orbitals and the other electronic orbitals are also explored. This general approachmore » enables computationally tractable yet accurate calculations on molecular systems with quantum protons. The RXCHF method is applied to the hydrogen cyanide (HCN) and FHF{sup −} systems, where the proton and all electrons are treated quantum mechanically. For the HCN system, only the two electronic orbitals associated with the CH covalent bond are geminal-coupled to the proton orbital. For the FHF{sup −} system, only the four electronic orbitals associated with the two FH covalent bonds are geminal-coupled to the proton orbital. For both systems, the RXCHF method produces qualitatively accurate nuclear densities, in contrast to mean field-based NEO approaches. The development and implementation of the RXCHF method provide the framework to perform calculations on systems such as proton-coupled electron transfer reactions, where electron-proton nonadiabatic effects are important.« less

Practical quantum key distribution protocol without monitoring signal disturbance.

PubMed

Sasaki, Toshihiko; Yamamoto, Yoshihisa; Koashi, Masato

2014-05-22

Quantum cryptography exploits the fundamental laws of quantum mechanics to provide a secure way to exchange private information. Such an exchange requires a common random bit sequence, called a key, to be shared secretly between the sender and the receiver. The basic idea behind quantum key distribution (QKD) has widely been understood as the property that any attempt to distinguish encoded quantum states causes a disturbance in the signal. As a result, implementation of a QKD protocol involves an estimation of the experimental parameters influenced by the eavesdropper's intervention, which is achieved by randomly sampling the signal. If the estimation of many parameters with high precision is required, the portion of the signal that is sacrificed increases, thus decreasing the efficiency of the protocol. Here we propose a QKD protocol based on an entirely different principle. The sender encodes a bit sequence onto non-orthogonal quantum states and the receiver randomly dictates how a single bit should be calculated from the sequence. The eavesdropper, who is unable to learn the whole of the sequence, cannot guess the bit value correctly. An achievable rate of secure key distribution is calculated by considering complementary choices between quantum measurements of two conjugate observables. We found that a practical implementation using a laser pulse train achieves a key rate comparable to a decoy-state QKD protocol, an often-used technique for lasers. It also has a better tolerance of bit errors and of finite-sized-key effects. We anticipate that this finding will give new insight into how the probabilistic nature of quantum mechanics can be related to secure communication, and will facilitate the simple and efficient use of conventional lasers for QKD.

Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions

PubMed Central

Dzierlenga, M.W.; Varga, M.J.

2016-01-01

The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). It was found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. It was found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs, and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics. PMID:27497161

Quantum-mechanical approach to predissociation of water dimers in the vibrational adiabatic representation: Importance of channel interactions.

PubMed

Mineo, H; Niu, Y L; Kuo, J L; Lin, S H; Fujimura, Y

2015-08-28

The results of application of the quantum-mechanical adiabatic theory to vibrational predissociation (VPD) of water dimers, (H2O)2 and (D2O)2, are presented. We consider the VPD processes including the totally symmetric OH mode of the dimer and the bending mode of the fragment. The VPD in the adiabatic representation is induced by breakdown of the vibrational adiabatic approximation, and two types of nonadiabatic coupling matrix elements are involved: one provides the VPD induced by the low-frequency dissociation mode and the other provides the VPD through channel interactions induced by the low-frequency modes. The VPD rate constants were calculated using the Fermi golden rule expression. A closed form for the nonadiabatic transition matrix element between the discrete and continuum states was derived in the Morse potential model. All of the parameters used were obtained from the potential surfaces of the water dimers, which were calculated by the density functional theory procedures. The VPD rate constants for the two processes were calculated in the non-Condon scheme beyond the so-called Condon approximation. The channel interactions in and between the initial and final states were taken into account, and those are found to increase the VPD rates by 3(1) orders of magnitude for the VPD processes in (H2O)2 ((D2O)2). The fraction of the bending-excited donor fragments is larger than that of the bending-excited acceptor fragments. The results obtained by quantum-mechanical approach are compared with both experimental and quasi-classical trajectory calculation results.

Nonparadoxical loss of information in black hole evaporation in a quantum collapse model

NASA Astrophysics Data System (ADS)

Modak, Sujoy K.; Ortíz, Leonardo; Peña, Igor; Sudarsky, Daniel

2015-06-01

We consider a novel approach to address the black hole information paradox. The idea is based on adapting, to the situation at hand, the modified versions of quantum theory involving spontaneous stochastic dynamical collapse of quantum states, which have been considered in attempts to deal with shortcomings of the standard Copenhagen interpretation of quantum mechanics, in particular, the issue known as "the measurement problem." The new basic hypothesis is that the modified quantum behavior is enhanced in the region of high curvature so that the information encoded in the initial quantum state of the matter fields is rapidly erased as the black hole singularity is approached. We show that in this manner the complete evaporation of the black hole via Hawking radiation can be understood as involving no paradox. Calculations are performed using a modified version of quantum theory known as "continuous spontaneous localization" (CSL), which was originally developed in the context of many-particle nonrelativistic quantum mechanics. We use a version of CSL tailored to quantum field theory and applied in the context of the two -dimensional Callan-Giddings-Harvey-Strominger model. Although the role of quantum gravity in this picture is restricted to the resolution of the singularity, related studies suggest that there might be further connections.

Interface and photoluminescence characteristics of graphene-(GaN/InGaN){sub n} multiple quantum wells hybrid structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Liancheng, E-mail: wanglc@semi.ac.cn, E-mail: lzq@semi.ac.cn, E-mail: zh.zhang@hebut.edu.cn; Semiconductor Lighting Technology Research and Development Center, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083; Mind Star

The effects of graphene on the optical properties of active system, e.g., the InGaN/GaN multiple quantum wells, are thoroughly investigated and clarified. Here, we have investigated the mechanisms accounting for the photoluminescence reduction for the graphene covered GaN/InGaN multiple quantum wells hybrid structure. Compared to the bare multiple quantum wells, the photoluminescence intensity of graphene covered multiple quantum wells showed a 39% decrease after excluding the graphene absorption losses. The responsible mechanisms have been identified with the following factors: (1) the graphene two dimensional hole gas intensifies the polarization field in multiple quantum wells, thus steepening the quantum well bandmore » profile and causing hole-electron pairs to further separate; (2) a lower affinity of graphene compared to air leading to a weaker capability to confine the excited hot electrons in multiple quantum wells; and (3) exciton transfer through non-radiative energy transfer process. These factors are theoretically analysed based on advanced physical models of semiconductor devices calculations and experimentally verified by varying structural parameters, such as the indium fraction in multiple quantum wells and the thickness of the last GaN quantum barrier spacer layer.« less

Quantum Mechanical Calculations in Collaborations with Experimental Chemistry: The Theoretical Organic Chemistry Perspective

NASA Astrophysics Data System (ADS)

Nguyen, Quynh Nhu Ngoc

The results of quantum chemical calculations reveal that polyanionic gallium-based cages accelerate cyclization reactions of pentadienyl alcohols by significantly increasing basicity of the substrate hydroxyl group. The energy barrier for cyclization of the pentadienyl cation after water loss is already low in the background reaction and is altered fairly little by the cage. The calculations for other non-alcohol substrates also suggest that the cage increases the basicity of amine and phosphine groups, though to a lesser extend comparing to the alcohol substrate. Due to their twisting patterns, alpha-helical peptides are known to have overall "macrodipoles" along the principal axes as the result of the backbone carbonyl groups pointing toward the C-terminus. As the dipoles have implications in helical bundles, interactions with lipid bilayers, and distribution of charge, chemists have long been interested in employing the macrodipole in modifications of peptides' catalytic activities. In this studied, we examined the impact of both global and local noncovalent interactions between peptide catalysts and substrates in the first transesterification step, in hope of designing a better peptide catalysts to aid in ester metabolism. Quantum mechanical calculations helped predict whether the targeted medium-sized cyclic peptide products would more likely be the major products, before the experimental team invested extensive resources and time to carry out the syntheses. Many systems were found to favor the medium-sized cyclic peptides, whereas one system was predicted to result in polycyclic product, and the latter experimental observations agreed with these predictions. Naturally occurring cyclic peptides display various biological activities due to their diverse structures. Understanding the dominant structures of these peptides could help give insight into protein-protein interactions or substrate-protein binding. With the experimental NMR data obtained for the synthesized peptides, dynamic simulations were used to sample a large conformational space, generating diverse conformer libraries. Quantum mechanical calculations were then used to determine the relative energies between the conformers, and to compute theoretical NMR data, which were then compared to the experimental values, to determine the best match conformers. Hydropersulfides are commonly found among many mammalian systems, and has recently gained more interest due to their greater nucleophilicity and reducing capacity compared to the related thiols. A series of quantum mechanical calculations were performed for small sulfur-containing molecules in order to help understand these biological compounds. First part of this chapter explores the basics of chemical properties and reactivity of hydropersulfides. The later sections further discuss the redox component of RSSH in generation of the radical RSS, which was found to be unreactive in the presence of O 2 and NO. Modeling the formation of these natural products in the absence of the enzymes has many of its own limitation, but understanding the inherent reactivity of the substrates could be beneficial to future enzymatic studies. Density functional theory calculations of mechanism of caryolene featured one mechanism with a base-catalyzed deprotonation/reprotonation sequence, while the other higher-energy mechanism involved intramolecular proton transfer and a secondary carbocation minimum. This result suggested the role of the enzyme in helping to avoid the secondary carbocation. Both pathways bypassed the concerted suprafacial/suprafacial [2+2] cycloadditions, which were not in violation of orbital symmetry due to their asynchronicity. Quantum mechanical calculations were used to determine theoretical 1H and 13C chemical shifts, which were then compared to the experimental NMR data to assign relative configurations for isohirsut-1-ene, isohirsut-4-ene, and tsukubadiene, which were previously isolated from engineered Streptomyces. Conformational searches and Boltzmann averaging were performed to address conformational flexibility in experimental NMR. The reactivity of macrocyclic bis-enones in Diels-Alder reactions was examined with quantum mechanical calculations to locate transition state structures and potential energy surfaces. Stepwise mechanisms appeared to be much lower in energy than the concerted pathways. Steric interactions and torsional strain helped explain product formations and why reactants that differed only by Z/E stereochemistry gave different product observation. The Ready group investigated the different approach to synthesizing nitrogen-containing heterocycles via dihydropyridine boronic ester intermediates, which was formed when pyridine boronic ester reacted with organometallic reagents in the presence of an acylating agent. The relative stereochemistry was initially assigned by comparison of experimental and computed chemical shifts, and the structure of the major product was later confirmed by X-ray crystallography. In the development of a stereo-controlled synthesis of australifungin, a natural products, only a small amount of the intermediate, which needed to undergo removal of protecting groups to yield the desired product, was obtained. There were worries that removing these protecting group might instead lead to undesired side product. However, the calculation results indicated that the desired product would still be more thermodynamically favored, giving confidence for the experimental work to proceed. (Abstract shortened by ProQuest.).

Dilepton production from hot hadronic matter in nonequilibrium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schenke, B.; Greiner, C.

2006-03-15

The influence of time-dependent medium modifications of low-mass vector mesons on dilepton production is investigated within a nonequilibrium quantum field-theoretical description on the basis of the Kadanoff-Baym equations. Time scales for the adaption of the spectral properties to changing self-energies are given, and, under use of a model for the fireball evolution, nonequilibrium dilepton yields from the decay of {rho} and {omega} mesons are calculated. In a comparison of these yields, those from calculations that assume instantaneous (Markovian) adaption to the changing-medium quantum-mechanical memory effects turn out to be important.

Quantum mechanical force field for water with explicit electronic polarization.

PubMed

Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

2013-08-07

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

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

ERIC Educational Resources Information Center

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

2012-01-01

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

Development of a quantum mechanics-based free-energy perturbation method: use in the calculation of relative solvation free energies.

PubMed

Reddy, M Rami; Singh, U C; Erion, Mark D

2004-05-26

Free-energy perturbation (FEP) is considered the most accurate computational method for calculating relative solvation and binding free-energy differences. Despite some success in applying FEP methods to both drug design and lead optimization, FEP calculations are rarely used in the pharmaceutical industry. One factor limiting the use of FEP is its low throughput, which is attributed in part to the dependence of conventional methods on the user's ability to develop accurate molecular mechanics (MM) force field parameters for individual drug candidates and the time required to complete the process. In an attempt to find an FEP method that could eventually be automated, we developed a method that uses quantum mechanics (QM) for treating the solute, MM for treating the solute surroundings, and the FEP method for computing free-energy differences. The thread technique was used in all transformations and proved to be essential for the successful completion of the calculations. Relative solvation free energies for 10 structurally diverse molecular pairs were calculated, and the results were in close agreement with both the calculated results generated by conventional FEP methods and the experimentally derived values. While considerably more CPU demanding than conventional FEP methods, this method (QM/MM-based FEP) alleviates the need for development of molecule-specific MM force field parameters and therefore may enable future automation of FEP-based calculations. Moreover, calculation accuracy should be improved over conventional methods, especially for calculations reliant on MM parameters derived in the absence of experimental data.

 The application of computational chemistry to lignin

Treesearch

Thomas Elder; Laura Berstis; Nele Sophie Zwirchmayr; Gregg T. Beckham; Michael F. Crowley

2017-01-01

Computational chemical methods have become an important technique in the examination of the structure and reactivity of lignin. The calculations can be based either on classical or quantum mechanics, with concomitant differences in computational intensity and size restrictions. The current paper will concentrate on results developed from the latter type of calculations...

The Heat Capacity of Ideal Gases

ERIC Educational Resources Information Center

Scott, Robert L.

2006-01-01

The heat capacity of an ideal gas has been shown to be calculable directly by statistical mechanics if the energies of the quantum states are known. However, unless one makes careful calculations, it is not easy for a student to understand the qualitative results. Why there are maxima (and occasionally minima) in heat capacity-temperature curves…

Possible Peroxo State of the Dicopper Site of Particulate Methane Monooxygenase from Combined Quantum Mechanics and Molecular Mechanics Calculations.

PubMed

Itoyama, Shuhei; Doitomi, Kazuki; Kamachi, Takashi; Shiota, Yoshihito; Yoshizawa, Kazunari

2016-03-21

Enzymatic methane hydroxylation is proposed to efficiently occur at the dinuclear copper site of particulate methane monooxygenase (pMMO), which is an integral membrane metalloenzyme in methanotrophic bacteria. The resting state and a possible peroxo state of the dicopper active site of pMMO are discussed by using combined quantum mechanics and molecular mechanics calculations on the basis of reported X-ray crystal structures of the resting state of pMMO by Rosenzweig and co-workers. The dicopper site has a unique structure, in which one copper is coordinated by two histidine imidazoles and another is chelated by a histidine imidazole and primary amine of an N-terminal histidine. The resting state of the dicopper site is assignable to the mixed-valent Cu(I)Cu(II) state from a computed Cu-Cu distance of 2.62 Å from calculations at the B3LYP-D/TZVP level of theory. A μ-η(2):η(2)-peroxo-Cu(II)2 structure similar to those of hemocyanin and tyrosinase is reasonably obtained by using the resting state structure and dioxygen. Computed Cu-Cu and O-O distances are 3.63 and 1.46 Å, respectively, in the open-shell singlet state. Structural features of the dicopper peroxo species of pMMO are compared with those of hemocyanin and tyrosinase and synthetic dicopper model compounds. Optical features of the μ-η(2):η(2)-peroxo-Cu(II)2 state are calculated and analyzed with TD-DFT calculations.

Virtually going green: The role of quantum computational chemistry in reducing pollution and toxicity in chemistry

NASA Astrophysics Data System (ADS)

Stevens, Jonathan

2017-07-01

Continuing advances in computational chemistry has permitted quantum mechanical calculation to assist in research in green chemistry and to contribute to the greening of chemical practice. Presented here are recent examples illustrating the contribution of computational quantum chemistry to green chemistry, including the possibility of using computation as a green alternative to experiments, but also illustrating contributions to greener catalysis and the search for greener solvents. Examples of applications of computation to ambitious projects for green synthetic chemistry using carbon dioxide are also presented.

Dynamic acousto-optic control of a strongly coupled photonic molecule

PubMed Central

Kapfinger, Stephan; Reichert, Thorsten; Lichtmannecker, Stefan; Müller, Kai; Finley, Jonathan J.; Wixforth, Achim; Kaniber, Michael; Krenner, Hubert J.

2015-01-01

Strongly confined photonic modes can couple to quantum emitters and mechanical excitations. To harness the full potential in quantum photonic circuits, interactions between different constituents have to be precisely and dynamically controlled. Here, a prototypical coupled element, a photonic molecule defined in a photonic crystal membrane, is controlled by a radio frequency surface acoustic wave. The sound wave is tailored to deliberately switch on and off the bond of the photonic molecule on sub-nanosecond timescales. In time-resolved experiments, the acousto-optically controllable coupling is directly observed as clear anticrossings between the two nanophotonic modes. The coupling strength is determined directly from the experimental data. Both the time dependence of the tuning and the inter-cavity coupling strength are found to be in excellent agreement with numerical calculations. The demonstrated mechanical technique can be directly applied for dynamic quantum gate operations in state-of-the-art-coupled nanophotonic, quantum cavity electrodynamic and optomechanical systems. PMID:26436203

Electrically driven spin qubit based on valley mixing

NASA Astrophysics Data System (ADS)

Huang, Wister; Veldhorst, Menno; Zimmerman, Neil M.; Dzurak, Andrew S.; Culcer, Dimitrie

2017-02-01

The electrical control of single spin qubits based on semiconductor quantum dots is of great interest for scalable quantum computing since electric fields provide an alternative mechanism for qubit control compared with magnetic fields and can also be easier to produce. Here we outline the mechanism for a drastic enhancement in the electrically-driven spin rotation frequency for silicon quantum dot qubits in the presence of a step at a heterointerface. The enhancement is due to the strong coupling between the ground and excited states which occurs when the electron wave function overcomes the potential barrier induced by the interface step. We theoretically calculate single qubit gate times tπ of 170 ns for a quantum dot confined at a silicon/silicon-dioxide interface. The engineering of such steps could be used to achieve fast electrical rotation and entanglement of spin qubits despite the weak spin-orbit coupling in silicon.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gets, A. V.; Krainov, V. P., E-mail: vpkrainov@mail.ru

The conductivity of single-walled carbon nanotubes at low temperatures is calculated. It is shown that it is much higher than the well-known conductivity of a model 1D Fermi system. This is a purely quantum-mechanical effect.

Strain-induced formation of fourfold symmetric SiGe quantum dot molecules.

PubMed

Zinovyev, V A; Dvurechenskii, A V; Kuchinskaya, P A; Armbrister, V A

2013-12-27

The strain field distribution at the surface of a multilayer structure with disklike SiGe nanomounds formed by heteroepitaxy is exploited to arrange the symmetric quantum dot molecules typically consisting of four elongated quantum dots ordered along the [010] and [100] directions. The morphological transition from fourfold quantum dot molecules to continuous fortresslike quantum rings with an increasing amount of deposited Ge is revealed. We examine key mechanisms underlying the formation of lateral quantum dot molecules by using scanning tunneling microscopy and numerical calculations of the strain energy distribution on the top of disklike SiGe nanomounds. Experimental data are well described by a simple thermodynamic model based on the accurate evaluation of the strain dependent part of the surface chemical potential. The spatial arrangement of quantum dots inside molecules is attributed to the effect of elastic property anisotropy.

Destructive interferences results in bosons anti bunching: refining Feynman's argument

NASA Astrophysics Data System (ADS)

Marchewka, Avi; Granot, Er'el

2014-09-01

The effect of boson bunching is frequently mentioned and discussed in the literature. This effect is the manifestation of bosons tendency to "travel" in clusters. One of the core arguments for boson bunching was formulated by Feynman in his well-known lecture series and has been frequently used ever since. By comparing the scattering probabilities of two bosons and of two distinguishable particles, he concluded: "We have the result that it is twice as likely to find two identical Bose particles scattered into the same state as you would calculate assuming the particles were different" [R.P. Feynman, R.B. Leighton, M. Sands, The Feynman Lectures on Physics: Quantum mechanics (Addison-Wesley, 1965)]. This argument was rooted in the scientific community (see for example [C. Cohen-Tannoudji, B. Diu, F. Laloë, Quantum Mechanics (John Wiley & Sons, Paris, 1977); W. Pauli, Exclusion Principle and Quantum Mechanics, Nobel Lecture (1946)]), however, while this sentence is completely valid, as is proved in [C. Cohen-Tannoudji, B. Diu, F. Laloë, Quantum Mechanics (John Wiley & Sons, Paris, 1977)], it is not a synonym of bunching. In fact, as it is shown in this paper, wherever one of the wavefunctions has a zero, bosons can anti-bunch and fermions can bunch. It should be stressed that zeros in the wavefunctions are ubiquitous in Quantum Mechanics and therefore the effect should be common. Several scenarios are suggested to witness the effect.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers.

PubMed

Reimers, Jeffrey R; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J J; Hendriksen, Bas L M; Elemans, Johannes A A W; Hush, Noel S; Crossley, Maxwell J

2015-11-10

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

PubMed

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Theoretical and Experimental Study of Inclusion Complexes of β-Cyclodextrins with Chalcone and 2',4'-Dihydroxychalcone.

PubMed

Sancho, Matias I; Andujar, Sebastian; Porasso, Rodolfo D; Enriz, Ricardo D

2016-03-31

The inclusion complexes formed by chalcone and 2',4'-dihydroxychalcone with β-cyclodextrin have been studied combining experimental (phase solubility diagrams, Fourier transform infrared spectroscopy) and molecular modeling (molecular dynamics, quantum mechanics/molecular mechanics calculations) techniques. The formation constants of the complexes were determined at different temperatures, and the thermodynamic parameters of the process were obtained. The inclusion of chalcone in β-cyclodextrin is an exothermic process, while the inclusion of 2',4'-dihydroxychalcone is endothermic. Free energy profiles, derived from umbrella sampling using molecular dynamics simulations, were constructed to analyze the binding affinity and the complexation reaction at a molecular level. Hybrid QM/MM calculations were also employed to obtain a better description of the energetic and structural aspects of the complexes. The intermolecular interactions that stabilize both inclusion complexes were characterized by means of quantum atoms in molecules theory and reduce density gradient method. The calculated interactions were experimentally observed using FTIR.

Quantum chemical modeling of the inhibition mechanism of monoamine oxidase by oxazolidinone and analogous heterocyclic compounds.

PubMed

Erdem, Safiye Sağ; Özpınar, Gül Altınbaş; Boz, Ümüt

2014-02-01

Monoamine oxidase (MAO, EC 1.4.3.4) is responsible from the oxidation of a variety of amine neurotransmitters. MAO inhibitors are used for the treatment of depression or Parkinson's disease. They also inhibit the catabolism of dietary amines. According to one hypothesis, inactivation results from the formation of a covalent adduct to a cysteine residue in the enzyme. If the adduct is stable enough, the enzyme is inhibited for a long time. After a while, enzyme can turn to its active form as a result of adduct breakdown by β-elimination. In this study, the proposed inactivation mechanism was modeled and tested by quantum chemical calculations. Eight heterocyclic methylthioamine derivatives were selected to represent the proposed covalent adducts. Activation energies related to their β-elimination reactions were calculated using ab initio and density functional theory methods. Calculated activation energies were in good agreement with the relative stabilities of the hypothetical adducts predicted in the literature by enzyme inactivation measurements.

Bistability and displacement fluctuations in a quantum nanomechanical oscillator

NASA Astrophysics Data System (ADS)

Avriller, R.; Murr, B.; Pistolesi, F.

2018-04-01

Remarkable features have been predicted for the mechanical fluctuations at the bistability transition of a classical oscillator coupled capacitively to a quantum dot [Micchi et al., Phys. Rev. Lett. 115, 206802 (2015), 10.1103/PhysRevLett.115.206802]. These results have been obtained in the regime ℏ ω0≪kBT ≪ℏ Γ , where ω0, T , and Γ are the mechanical resonating frequency, the temperature, and the tunneling rate, respectively. A similar behavior could be expected in the quantum regime of ℏ Γ ≪kBT ≪ℏ ω0 . We thus calculate the energy- and displacement-fluctuation spectra and study their behavior as a function of the electromechanical coupling constant when the system enters the Frank-Condon regime. We find that in analogy with the classical case, the energy-fluctuation spectrum and the displacement spectrum widths show a maximum for values of the coupling constant at which a mechanical bistability is established.

Giant photocurrent enhancement by transition metal doping in quantum dot sensitized solar cells

NASA Astrophysics Data System (ADS)

Rimal, Gaurab; Pimachev, Artem K.; Yost, Andrew J.; Poudyal, Uma; Maloney, Scott; Wang, Wenyong; Chien, TeYu; Dahnovsky, Yuri; Tang, Jinke

2016-09-01

A huge enhancement in the incident photon-to-current efficiency of PbS quantum dot (QD) sensitized solar cells by manganese doping is observed. In the presence of Mn dopants with relatively small concentration (4 at. %), the photoelectric current increases by an average of 300% (up to 700%). This effect cannot be explained by the light absorption mechanism because both the experimental and theoretical absorption spectra demonstrate several times decreases in the absorption coefficient. To explain such dramatic increase in the photocurrent we propose the electron tunneling mechanism from the LUMO of the QD excited state to the Zn2SnO4 (ZTO) semiconductor photoanode. This change is due to the presence of the Mn instead of Pb atom at the QD/ZTO interface. The ab initio calculations confirm this mechanism. This work proposes an alternative route for a significant improvement of the efficiency for quantum dot sensitized solar cells.

Realistic clocks, universal decoherence, and the black hole information paradox.

PubMed

Gambini, Rodolfo; Porto, Rafael A; Pullin, Jorge

2004-12-10

Ordinary quantum mechanics is formulated on the basis of the existence of an ideal classical clock external to the system under study. This is clearly an idealization. As emphasized originally by Salecker and Wigner and more recently by others, there exist limits in nature to how "classical" even the best possible clock can be. With realistic clocks, quantum mechanics ceases to be unitary and a fundamental mechanism of decoherence of quantum states arises. We estimate the rate of the universal loss of unitarity using optimal realistic clocks. In particular, we observe that the rate is rapid enough to eliminate the black hole information puzzle: all information is lost through the fundamental decoherence before the black hole can evaporate. This improves on a previous calculation we presented with a suboptimal clock in which only part of the information was lost by the time of evaporation.

Quantum mechanical, spectroscopic study (FT-IR and FT - Raman), NBO analysis, HOMO-LUMO, first order hyperpolarizability and docking studies of a non-steroidal anti-inflammatory compound

NASA Astrophysics Data System (ADS)

Sakthivel, S.; Alagesan, T.; Muthu, S.; Abraham, Christina Susan; Geetha, E.

2018-03-01

Experimental and theoretical studies on the optimized geometrical structure, electronic and vibrational characteristics of (+)-(S)-2-(6-methoxynaphthalen-2-yl) propanoic acid are presented employing B3LYP/6-311++G (d,p) basis set. Simulated FT-IR and FT-Raman spectra were in concurrence with the observed spectra attained in a spectral range of FT-IR (4000 - 400 cm-1) and FT-Raman (4000 - 100 cm-1). Quantum chemical calculations and the comprehensive vibrational assignments of wavenumbers of the optimized geometry using Potential Energy Distribution (PED) were calculated with scaled quantum mechanics. The infrared intensities and Raman intensities of (+)-(S)-2-(6-methoxynaphthalen-2-yl) propanoic acid were reported. Frontier molecular orbital analysis and reactivity parameters were calculated. Molecular Electrostatic Potential (MEP), Natural Bond Orbital (NBO) analysis, Non Linear Optical (NLO) behavior and thermodynamic properties were studied. In addition, the Mulliken charge distribution and Fukui function were analyzed. Molecular docking was used to dock in the title molecule into the active site of the protein 5L9B which belongs to the class of proteins exhibiting the property as a HIF1A (Hypoxia-inducible factor 1-alpha) expression inhibitor and the minimum binding energy was detected to be -6.2 kcal/mol.

Classical theory of atomic collisions - The first hundred years

NASA Astrophysics Data System (ADS)

Grujić, Petar V.

2012-05-01

Classical calculations of the atomic processes started in 1911 with famous Rutherford's evaluation of the differential cross section for α particles scattered on foil atoms [1]. The success of these calculations was soon overshadowed by the rise of Quantum Mechanics in 1925 and its triumphal success in describing processes at the atomic and subatomic levels. It was generally recognized that the classical approach should be inadequate and it was neglected until 1953, when the famous paper by Gregory Wannier appeared, in which the threshold law for the single ionization cross section behaviour by electron impact was derived. All later calculations and experimental studies confirmed the law derived by purely classical theory. The next step was taken by Ian Percival and collaborators in 60s, who developed a general classical three-body computer code, which was used by many researchers in evaluating various atomic processes like ionization, excitation, detachment, dissociation, etc. Another approach was pursued by Michal Gryzinski from Warsaw, who started a far reaching programme for treating atomic particles and processes as purely classical objects [2]. Though often criticized for overestimating the domain of the classical theory, results of his group were able to match many experimental data. Belgrade group was pursuing the classical approach using both analytical and numerical calculations, studying a number of atomic collisions, in particular near-threshold processes. Riga group, lead by Modris Gailitis [3], contributed considerably to the field, as it was done by Valentin Ostrovsky and coworkers from Sanct Petersbourg, who developed powerful analytical methods within purely classical mechanics [4]. We shall make an overview of these approaches and show some of the remarkable results, which were subsequently confirmed by semiclassical and quantum mechanical calculations, as well as by the experimental evidence. Finally we discuss the theoretical and epistemological background of the classical calculations and explain why these turned out so successful, despite the essentially quantum nature of the atomic and subatomic systems.

Energetic factors determining the binding of type I inhibitors to c-Met kinase: experimental studies and quantum mechanical calculations.

PubMed

Yu, Zhe; Ma, Yu-chi; Ai, Jing; Chen, Dan-qi; Zhao, Dong-mei; Wang, Xin; Chen, Yue-lei; Geng, Mei-yu; Xiong, Bing; Cheng, Mao-sheng; Shen, Jing-Kang

2013-11-01

To decipher the molecular interactions between c-Met and its type I inhibitors and to facilitate the design of novel c-Met inhibitors. Based on the prototype model inhibitor 1, four ligands with subtle differences in the fused aromatic rings were synthesized. Quantum chemistry was employed to calculate the binding free energy for each ligand. Symmetry-adapted perturbation theory (SAPT) was used to decompose the binding energy into several fundamental forces to elucidate the determinant factors. Binding free energies calculated from quantum chemistry were correlated well with experimental data. SAPT calculations showed that the predominant driving force for binding was derived from a sandwich π-π interaction with Tyr-1230. Arg-1208 was the differentiating factor, interacting with the 6-position of the fused aromatic ring system through the backbone carbonyl with a force pattern similar to hydrogen bonding. Therefore, a hydrogen atom must be attached at the 6-position, and changing the carbon atom to nitrogen caused unfavorable electrostatic interactions. The theoretical studies have elucidated the determinant factors involved in the binding of type I inhibitors to c-Met.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

NASA Astrophysics Data System (ADS)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

2017-12-01

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

PubMed

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Instructional Approach to Molecular Electronic Structure Theory

ERIC Educational Resources Information Center

Dykstra, Clifford E.; Schaefer, Henry F.

1977-01-01

Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

Structural characterization of metal complexes in aqueous solutions: a XAS study of stannous fluoride

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alsina, Marco A.; Gaillard, Jean-François

The identity and structure of tin(ii)-fluoride complexes formed in aqueous solutions are determined by combining X-ray absorption spectroscopy, thermodynamic modeling and quantum mechanical calculations.

The polarizability of diatomic helium. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Fortune, P. J.

1974-01-01

The calculation of the electric dipole polarizability tensor of the He 2 dimer is described, and the results are used in the computation of several dielectric and optical properties of helium gas, at both high (322 K) and low (4 K) temperatures. The properties considered are the second dielectric virial coefficient, the second Kerr virial coefficient, and the depolarization ratio of the integrated intensities for the Raman scattering experiments. The thesis consists of five parts: the polarizability and various properties are defined; the calculation of the polarizability in the long-range region in terms of a quantum mechanical multipole expansion is described; the calculation of the He2 polarizability in the overlap region via coupled Hartree-Fock perturbation theory is described; the calculation of the quantum pair distribution function for both the He-3 and He-4 isotopes at 4 K is discussed; and the calculated values of the properties of helium gas are given.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene III. 3,3-Dimethyl-1-(trimethylsilyl)cyclopropene

NASA Astrophysics Data System (ADS)

De Maré, G. R.; Panchenko, Yu. N.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2003-07-01

The experimental Raman and IR vibrational spectra of 3,3-dimethyl-1-(trimethylsilyl)cyclopropene in the liquid phase were recorded. Total geometry optimisation was carried out at the HF/6-31G* level and the HF/6-31G*//HF/6-31G* force field was computed. This force field was corrected by scale factors determined previously (using Pulay's method) for correction of the HF/6-31G*//HF/6-31G* force fields of 3,3-dimethylbutene-1, 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The theoretical vibrational frequencies calculated from the scaled quantum mechanical force field and the theoretical intensities obtained from the quantum mechanical calculation were used to construct predicted spectra and to perform the vibrational analysis of the experimental spectra.

A quantum mechanical strategy to investigate the structure of liquids: the cases of acetonitrile, formamide, and their mixture.

PubMed

Mennucci, Benedetta; da Silva, Clarissa O

2008-06-05

A computational strategy based on quantum mechanical (QM) calculations and continuum solvation models is used to investigate the structure of liquids (either neat liquids or mixtures). The strategy is based on the comparison of calculated and experimental spectroscopic properties (IR-Raman vibrational frequencies and Raman intensities). In particular, neat formamide, neat acetonitrile, and their equimolar mixture are studied comparing isolated and solvated clusters of different nature and size. In all cases, the study seems to indicate that liquids, even when strongly associated, can be effectively modeled in terms of a shell-like system in which clusters of strongly interacting molecules (the microenvironments) are solvated by a polarizable macroenvironment represented by the rest of the molecules. Only taking into proper account both these effects can a correct picture of the liquid structure be achieved.

Mixed QM/MM molecular electrostatic potentials.

PubMed

Hernández, B; Luque, F J; Orozco, M

2000-05-01

A new method is presented for the calculation of the Molecular Electrostatic Potential (MEP) in large systems. Based on the mixed Quantum Mechanics/Molecular Mechanics (QM/MM) approach, the method assumes both a quantum and classical description for the molecule, and the calculation of the MEP in the space surrounding the molecule is made using this dual treatment. The MEP at points close to the molecule is computed using a full QM formalism, while a pure classical evaluation of the MEP is used for points located at large distances from the molecule. The algorithm allows the user to select the desired level of accuracy in the MEP, so that the definition of the regions where the MEP is computed at the classical or QM levels is adjusted automatically. The potential use of this QM/MM MEP in molecular modeling studies is discussed.

Phosphorylation Reaction in cAPK Protein Kinase - Free Energy Quantum Mechanic/Molecular Mechanics Simulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valiev, Marat; Yang, Jie; Adams, Joseph

2007-11-29

Protein kinases catalyze the transfer of the γ-phosphoryl group from ATP, a key regulatory process governing signalling pathways in eukaryotic cells. The structure of the active site in these enzymes is highly conserved implying common catalytic mechanism. In this work we investigate the reaction process in cAPK protein kinase (PKA) using a combined quantum mechanics and molecular mechanics approach. The novel computational features of our work include reaction pathway determination with nudged elastic band methodology and calculation of free energy profiles of the reaction process taking into account finite temperature fluctuations of the protein environment. We find that the transfermore » of the γ-phosphoryl group in the protein environment is an exothermic reaction with the reaction barrier of 15 kcal/mol.« less

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

PubMed

Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

2016-06-30

In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level

PubMed Central

Olsson, Martin A.; Söderhjelm, Pär

2016-01-01

In this article, the convergence of quantum mechanical (QM) free‐energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa‐acid deep‐cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158–224 atoms). We use single‐step exponential averaging (ssEA) and the non‐Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi‐empirical PM6‐DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free‐energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27117350

Direct hydride shift mechanism and stereoselectivity of P450nor confirmed by QM/MM calculations.

PubMed

Krámos, Balázs; Menyhárd, Dóra K; Oláh, Julianna

2012-01-19

Nitric oxide reductase (P450(nor)) found in Fusarium oxysporum catalyzes the reduction of nitric oxide to N(2)O in a multistep process. The reducing agent, NADH, is bound in the distal pocket of the enzyme, and direct hydride transfer occurs from NADH to the nitric oxide bound heme enzyme, forming intermediate I. Here we studied the possibility of hydride transfer from NADH to both the nitrogen and oxygen of the heme-bound nitric oxide, using quantum chemical and combined quantum mechanics/molecular mechanics (QM/MM) calculations, on two different protein models, representing both possible stereochemistries, a syn- and an anti-NADH arrangement. All calculations clearly favor hydride transfer to the nitrogen of nitric oxide, and the QM-only barrier and kinetic isotope effects are good agreement with the experimental values of intermediate I formation. We obtained higher barriers in the QM/MM calculations for both pathways, but hydride transfer to the nitrogen of nitric oxide is still clearly favored. The barriers obtained for the syn, Pro-R conformation of NADH are lower and show significantly less variation than the barriers obtained in the case of anti conformation. The effect of basis set and wide range of functionals on the obtained results are also discussed.

Molecular Quantum Mechanics: Analytic Gradients and Beyond - Program and Abstracts

DTIC Science & Technology

2007-06-03

Kutzelnigg (Bochum, Germany) Chair: Pekka Pyykko (Helsinki, Finland) Which Masses are Vibrating or Rotating in a Molecule? 15:40-16:15 O30...Krylov (Los Angeles, CA, U.S.A.) Multiconfigurational Quantum Chemistry for Actinide Containing Systems: From Isolated Molecules to Condensed...the genetic algorithm will be critically assessed. For B4n, the double rings are notably stable. The DFT calculations provide strong indications of

Energy transfer mechanisms in layered 2D perovskites.

PubMed

Williams, Olivia F; Guo, Zhenkun; Hu, Jun; Yan, Liang; You, Wei; Moran, Andrew M

2018-04-07

Two-dimensional (2D) perovskite quantum wells are generating broad scientific interest because of their potential for use in optoelectronic devices. Recently, it has been shown that layers of 2D perovskites can be grown in which the average thicknesses of the quantum wells increase from the back to the front of the film. This geometry carries implications for light harvesting applications because the bandgap of a quantum well decreases as its thickness increases. The general structural formula for the 2D perovskite systems under investigation in this work is (PEA) 2 (MA) n-1 [Pb n I 3n+1 ] (PEA = phenethyl ammonium, MA = methyl ammonium). Here, we examine two layered 2D perovskites with different distributions of quantum well thicknesses. Spectroscopic measurements and model calculations suggest that both systems funnel electronic excitations from the back to the front of the film through energy transfer mechanisms on the time scales of 100's of ps (i.e., energy transfer from thinner to thicker quantum wells). In addition, the model calculations demonstrate that the transient absorption spectra are composed of a progression of single exciton and biexciton resonances associated with the individual quantum wells. We find that exciton dissociation and/or charge transport dynamics make only minor contributions to the transient absorption spectra within the first 1 ns after photo-excitation. An analysis of the energy transfer kinetics indicates that the transitions occur primarily between quantum wells with values of n that differ by 1 because of the spectral overlap factor that governs the energy transfer rate. Two-dimensional transient absorption spectra reveal a pattern of resonances consistent with the dominance of sequential energy transfer dynamics.

Energy transfer mechanisms in layered 2D perovskites

NASA Astrophysics Data System (ADS)

Williams, Olivia F.; Guo, Zhenkun; Hu, Jun; Yan, Liang; You, Wei; Moran, Andrew M.

2018-04-01

Two-dimensional (2D) perovskite quantum wells are generating broad scientific interest because of their potential for use in optoelectronic devices. Recently, it has been shown that layers of 2D perovskites can be grown in which the average thicknesses of the quantum wells increase from the back to the front of the film. This geometry carries implications for light harvesting applications because the bandgap of a quantum well decreases as its thickness increases. The general structural formula for the 2D perovskite systems under investigation in this work is (PEA)2(MA)n-1[PbnI3n+1] (PEA = phenethyl ammonium, MA = methyl ammonium). Here, we examine two layered 2D perovskites with different distributions of quantum well thicknesses. Spectroscopic measurements and model calculations suggest that both systems funnel electronic excitations from the back to the front of the film through energy transfer mechanisms on the time scales of 100's of ps (i.e., energy transfer from thinner to thicker quantum wells). In addition, the model calculations demonstrate that the transient absorption spectra are composed of a progression of single exciton and biexciton resonances associated with the individual quantum wells. We find that exciton dissociation and/or charge transport dynamics make only minor contributions to the transient absorption spectra within the first 1 ns after photo-excitation. An analysis of the energy transfer kinetics indicates that the transitions occur primarily between quantum wells with values of n that differ by 1 because of the spectral overlap factor that governs the energy transfer rate. Two-dimensional transient absorption spectra reveal a pattern of resonances consistent with the dominance of sequential energy transfer dynamics.

Dislocation-driven growth of two-dimensional lateral quantum-well superlattices

PubMed Central

Chen, Jianyi; Li, Dongdong

2018-01-01

The advent of two-dimensional (2D) materials has led to extensive studies of heterostructures for novel applications. 2D lateral multiheterojunctions and superlattices have been recently demonstrated, but the available growth methods can only produce features with widths in the micrometer or, at best, 100-nm scale and usually result in rough and defective interfaces with extensive chemical intermixing. Widths smaller than 5 nm, which are needed for quantum confinement effects and quantum-well applications, have not been achieved. We demonstrate the growth of sub–2-nm quantum-well arrays in semiconductor monolayers, driven by the climb of misfit dislocations in a lattice-mismatched sulfide/selenide heterointerface. Density functional theory calculations provide an atom-by-atom description of the growth mechanism. The calculated energy bands reveal type II alignment suitable for quantum wells, suggesting that the structure could, in principle, be turned into a “conduit” of conductive nanoribbons for interconnects in future 2D integrated circuits via n-type modulation doping. This misfit dislocation–driven growth can be applied to different combinations of 2D monolayers with lattice mismatch, paving the way to a wide range of 2D quantum-well superlattices with controllable band alignment and nanoscale width. PMID:29740600

Quantum mechanics/molecular mechanics modeling of covalent addition between EGFR-cysteine 797 and N-(4-anilinoquinazolin-6-yl) acrylamide.

PubMed

Capoferri, Luigi; Lodola, Alessio; Rivara, Silvia; Mor, Marco

2015-03-23

Irreversible epidermal growth factor receptor (EGFR) inhibitors can circumvent resistance to first-generation ATP-competitive inhibitors in the treatment of nonsmall-cell lung cancer. They covalently bind a noncatalytic cysteine (Cys797) at the surface of EGFR active site by an acrylamide warhead. Herein, we used a hybrid quantum mechanics/molecular mechanics (QM/MM) potential in combination with umbrella sampling in the path-collective variable space to investigate the mechanism of alkylation of Cys797 by the prototypical covalent inhibitor N-(4-anilinoquinazolin-6-yl) acrylamide. Calculations show that Cys797 reacts with the acrylamide group of the inhibitor through a direct addition mechanism, with Asp800 acting as a general base/general acid in distinct steps of the reaction. The obtained reaction free energy is negative (ΔA = -12 kcal/mol) consistent with the spontaneous and irreversible alkylation of Cys797 by N-(4-anilinoquinazolin-6-yl) acrylamide. Our calculations identify desolvation of Cys797 thiolate anion as a key step of the alkylation process, indicating that changes in the intrinsic reactivity of the acrylamide would have only a minor impact on the inhibitor potency.

Quantum Monte Carlo studies of solvated systems

NASA Astrophysics Data System (ADS)

Schwarz, Kathleen; Letchworth Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

2011-03-01

Solvation qualitatively alters the energetics of diverse processes from protein folding to reactions on catalytic surfaces. An explicit description of the solvent in quantum-mechanical calculations requires both a large number of electrons and exploration of a large number of configurations in the phase space of the solvent. These problems can be circumvented by including the effects of solvent through a rigorous classical density-functional description of the liquid environment, thereby yielding free energies and thermodynamic averages directly, while eliminating the need for explicit consideration of the solvent electrons. We have implemented and tested this approach within the CASINO Quantum Monte Carlo code. Our method is suitable for calculations in any basis within CASINO, including b-spline and plane wave trial wavefunctions, and is equally applicable to molecules, surfaces, and crystals. For our preliminary test calculations, we use a simplified description of the solvent in terms of an isodensity continuum dielectric solvation approach, though the method is fully compatible with more reliable descriptions of the solvent we shall employ in the future.

Book Review:

NASA Astrophysics Data System (ADS)

Louko, Jorma

2007-04-01

Bastianelli and van Nieuwenhuizen's monograph `Path Integrals and Anomalies in Curved Space' collects in one volume the results of the authors' 15-year research programme on anomalies that arise in Feynman diagrams of quantum field theories on curved manifolds. The programme was spurred by the path-integral techniques introduced in Alvarez-Gaumé and Witten's renowned 1983 paper on gravitational anomalies which, together with the anomaly cancellation paper by Green and Schwarz, led to the string theory explosion of the 1980s. The authors have produced a tour de force, giving a comprehensive and pedagogical exposition of material that is central to current research. The first part of the book develops from scratch a formalism for defining and evaluating quantum mechanical path integrals in nonlinear sigma models, using time slicing regularization, mode regularization and dimensional regularization. The second part applies this formalism to quantum fields of spin 0, 1/2, 1 and 3/2 and to self-dual antisymmetric tensor fields. The book concludes with a discussion of gravitational anomalies in 10-dimensional supergravities, for both classical and exceptional gauge groups. The target audience is researchers and graduate students in curved spacetime quantum field theory and string theory, and the aims, style and pedagogical level have been chosen with this audience in mind. Path integrals are treated as calculational tools, and the notation and terminology are throughout tailored to calculational convenience, rather than to mathematical rigour. The style is closer to that of an exceedingly thorough and self-contained review article than to that of a textbook. As the authors mention, the first part of the book can be used as an introduction to path integrals in quantum mechanics, although in a classroom setting perhaps more likely as supplementary reading than a primary class text. Readers outside the core audience, including this reviewer, will gain from the book a heightened appreciation of the central role of regularization as a defining ingredient of a quantum field theory and will be impressed by the agreement of results arising from different regularization schemes. The readers may in particular enjoy the authors' `brief history of anomalies' in quantum field theory, as well as a similar historical discussion of path integrals in quantum mechanics.

Nonadiabatic Molecular Dynamics and Orthogonality Constrained Density Functional Theory

NASA Astrophysics Data System (ADS)

Shushkov, Philip Georgiev

The exact quantum dynamics of realistic, multidimensional systems remains a formidable computational challenge. In many chemical processes, however, quantum effects such as tunneling, zero-point energy quantization, and nonadiabatic transitions play an important role. Therefore, approximate approaches that improve on the classical mechanical framework are of special practical interest. We propose a novel ring polymer surface hopping method for the calculation of chemical rate constants. The method blends two approaches, namely ring polymer molecular dynamics that accounts for tunneling and zero-point energy quantization, and surface hopping that incorporates nonadiabatic transitions. We test the method against exact quantum mechanical calculations for a one-dimensional, two-state model system. The method reproduces quite accurately the tunneling contribution to the rate and the distribution of reactants between the electronic states for this model system. Semiclassical instanton theory, an approach related to ring polymer molecular dynamics, accounts for tunneling by the use of periodic classical trajectories on the inverted potential energy surface. We study a model of electron transfer in solution, a chemical process where nonadiabatic events are prominent. By representing the tunneling electron with a ring polymer, we derive Marcus theory of electron transfer from semiclassical instanton theory after a careful analysis of the tunneling mode. We demonstrate that semiclassical instanton theory can recover the limit of Fermi's Golden Rule rate in a low-temperature, deep-tunneling regime. Mixed quantum-classical dynamics treats a few important degrees of freedom quantum mechanically, while classical mechanics describes affordably the rest of the system. But the interface of quantum and classical description is a challenging theoretical problem, especially for low-energy chemical processes. We therefore focus on the semiclassical limit of the coupled nuclear-electronic dynamics. We show that the time-dependent Schrodinger equation for the electrons employed in the widely used fewest switches surface hopping method is applicable only in the limit of nearly identical classical trajectories on the different potential energy surfaces. We propose a short-time decoupling algorithm that restricts the use of the Schrodinger equation only to the interaction regions. We test the short-time approximation on three model systems against exact quantum-mechanical calculations. The approximation improves the performance of the surface hopping approach. Nonadiabatic molecular dynamics simulations require the efficient and accurate computation of ground and excited state potential energy surfaces. Unlike the ground state calculations where standard methods exist, the computation of excited state properties is a challenging task. We employ time-independent density functional theory, in which the excited state energy is represented as a functional of the total density. We suggest an adiabatic-like approximation that simplifies the excited state exchange-correlation functional. We also derive a set of minimal conditions to impose exactly the orthogonality of the excited state Kohn-Sham determinant to the ground state determinant. This leads to an efficient, variational algorithm for the self-consistent optimization of the excited state energy. Finally, we assess the quality of the excitation energies obtained by the new method on a set of 28 organic molecules. The new approach provides results of similar accuracy to time-dependent density functional theory.

Reassessing the atmospheric oxidation mechanism of toluene

NASA Astrophysics Data System (ADS)

Ji, Yuemeng; Zhao, Jun; Terazono, Hajime; Misawa, Kentaro; Levitt, Nicholas P.; Li, Yixin; Lin, Yun; Peng, Jianfei; Wang, Yuan; Duan, Lian; Pan, Bowen; Zhang, Fang; Feng, Xidan; An, Taicheng; Marrero-Ortiz, Wilmarie; Secrest, Jeremiah; Zhang, Annie L.; Shibuya, Kazuhiko; Molina, Mario J.; Zhang, Renyi

2017-08-01

Photochemical oxidation of aromatic hydrocarbons leads to tropospheric ozone and secondary organic aerosol (SOA) formation, with profound implications for air quality, human health, and climate. Toluene is the most abundant aromatic compound under urban environments, but its detailed chemical oxidation mechanism remains uncertain. From combined laboratory experiments and quantum chemical calculations, we show a toluene oxidation mechanism that is different from the one adopted in current atmospheric models. Our experimental work indicates a larger-than-expected branching ratio for cresols, but a negligible formation of ring-opening products (e.g., methylglyoxal). Quantum chemical calculations also demonstrate that cresols are much more stable than their corresponding peroxy radicals, and, for the most favorable OH (ortho) addition, the pathway of H extraction by O2 to form the cresol proceeds with a smaller barrier than O2 addition to form the peroxy radical. Our results reveal that phenolic (rather than peroxy radical) formation represents the dominant pathway for toluene oxidation, highlighting the necessity to reassess its role in ozone and SOA formation in the atmosphere.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akdoğan, Ender, E-mail: ender.akdogan@tpe.gov.tr; Çiftçi, Muharrem, E-mail: muharrem-ciftci@windowslive.com

This article is based on the master thesis [4] related to our invention which was published in World Intellectual Property Organization (WO/2011/048506) as a microwave water heater. In the project, a prototype was produced to use microwave in industrial heating. In order to produce the prototype, the most appropriate material kind for microwave-water experiments was determined by a new energy loss rate calculation technique. This new energy loss calculation is a determinative factor for material permeability at microwave frequency band (1-100 GHz). This experimental series aim to investigate the rationality of using microwave in heating industry. Theoretically, heating water by microwavemore » (with steady frequency 2.45 GHz) is analyzed from sub-molecular to Classical Mechanic results of heating. In the study, we examined Quantum Mechanical base of heating water by microwave experiments. As a result, we derived a Semi-Quantum Mechanical equation for microwave-water interactions and thus, Wien displacement law can be derived to verify experimental observations by this equation.« less

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

PubMed

Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

2015-01-22

The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

Vibrational Heat Transport in Molecular Junctions

NASA Astrophysics Data System (ADS)

Segal, Dvira; Agarwalla, Bijay Kumar

2016-05-01

We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.

F + H2 collisions on two electronic potential energy surfaces - Quantum-mechanical study of the collinear reaction

NASA Technical Reports Server (NTRS)

Zimmerman, I. H.; Baer, M.; George, T. F.

1979-01-01

Collinear quantum calculations are carried out for reactive F + H2 collisions on two electronic potential energy surfaces. The resulting transmission and reflection probabilities exhibit much greater variation with energy than single-surface studies would lead us to anticipate. Transmission to low-lying product channels is increased by orders of magnitude by the presence of the second surface; however, branching ratios among product states are found to be independent of the initial electronic state of the reactants. These apparently contradictory aspects of the calculation are discussed and a tentative explanation put forward to resolve them.

Disulfides as Cyanide Antidotes: Evidence for a New In Vivo Oxidative Pathway for Cyanide Detoxification

DTIC Science & Technology

2009-01-01

the quantum mechanical calculations in this paper. M.A.Z. further thanks Drs. Clarence Broomfield and Alan Brimfield for their assistance on this... fluorescence . Eur. J. Biochem. 28, 89–93. (8) Leininger, K. R., and Westley, J. (1968) The mechanism of the rhodanese-catalyzed thiosulfate-cyanide

Plasmonic eigenmodes in individual and bow-tie graphene nanotriangles

NASA Astrophysics Data System (ADS)

Wang, Weihua; Christensen, Thomas; Jauho, Antti-Pekka; Thygesen, Kristian S.; Wubs, Martijn; Mortensen, N. Asger

2015-04-01

In classical electrodynamics, nanostructured graphene is commonly modeled by the computationally demanding problem of a three-dimensional conducting film of atomic-scale thickness. Here, we propose an efficient alternative two-dimensional electrostatic approach where all calculation procedures are restricted to the graphene sheet. Furthermore, to explore possible quantum effects, we perform tight-binding calculations, adopting a random-phase approximation. We investigate multiple plasmon modes in 20 nm equilateral triangles of graphene, treating the optical response classically as well as quantum mechanically. Compared to the classical plasmonic spectrum which is ``blind'' to the edge termination, we find that the quantum plasmon frequencies exhibit blueshifts in the case of armchair edge termination of the underlying atomic lattice, while redshifts are found for zigzag edges. Furthermore, we find spectral features in the zigzag case which are associated with electronic edge states not present for armchair termination. Merging pairs of triangles into dimers, plasmon hybridization leads to energy splitting that appears strongest in classical calculations while splitting is lower for armchair edges and even more reduced for zigzag edges. Our various results illustrate a surprising phenomenon: Even 20 nm large graphene structures clearly exhibit quantum plasmonic features due to atomic-scale details in the edge termination.

Fast summation of divergent series and resurgent transseries from Meijer-G approximants

NASA Astrophysics Data System (ADS)

Mera, Héctor; Pedersen, Thomas G.; Nikolić, Branislav K.

2018-05-01

We develop a resummation approach based on Meijer-G functions and apply it to approximate the Borel sum of divergent series and the Borel-Écalle sum of resurgent transseries in quantum mechanics and quantum field theory (QFT). The proposed method is shown to vastly outperform the conventional Borel-Padé and Borel-Padé-Écalle summation methods. The resulting Meijer-G approximants are easily parametrized by means of a hypergeometric ansatz and can be thought of as a generalization to arbitrary order of the Borel-hypergeometric method [Mera et al., Phys. Rev. Lett. 115, 143001 (2015), 10.1103/PhysRevLett.115.143001]. Here we demonstrate the accuracy of this technique in various examples from quantum mechanics and QFT, traditionally employed as benchmark models for resummation, such as zero-dimensional ϕ4 theory; the quartic anharmonic oscillator; the calculation of critical exponents for the N -vector model; ϕ4 with degenerate minima; self-interacting QFT in zero dimensions; and the summation of one- and two-instanton contributions in the quantum-mechanical double-well problem.

Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies.

PubMed

Strenalyuk, Tatyana; Samdal, Svein; Volden, Hans Vidar

2008-05-29

The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are very different for the two isomers.

Quantum mechanical study of solvent effects in a prototype S{sub N}2 reaction in solution: Cl{sup −} attack on CH{sub 3}Cl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; York, Darrin M., E-mail: york@biomaps.rutgers.edu

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype S{sub N}2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resultingmore » free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.« less

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; York, Darrin M.

2014-02-01

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

PubMed

Kuechler, Erich R; York, Darrin M

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Localized states in an arbitrarily bent quantum wire (bend-imitating approach)

NASA Astrophysics Data System (ADS)

Vakhnenko, Oleksity O.

1996-02-01

The bend-imitating matching technique is proposed to simplify the quantum mechanical treatment of singly and multiply bent 2D quantum wires of constant width, arbitrary bending angles, arbitrary bending radii and arbitrary distances between the bends. The spectrum of one-electron localized states and its dependence on the bending angle and the bending radius in a singly bent wire is explicitly calculated. Doubly bent wires are shown to possess doubly split localized states. The splitting energies as a function of the distance between the bends and the bending angles and bending radii have also been obtained. A similar description of bent 3D quantum wires and bent optical fibers is expected to be possible.

Epoxide reduction with hydrazine on graphene: a first principles study.

PubMed

Kim, Min Chan; Hwang, Gyeong S; Ruoff, Rodney S

2009-08-14

Mechanisms for epoxide reduction with hydrazine on a single-layer graphene sheet are examined using quantum mechanical calculations within the framework of gradient-corrected spin-polarized density-functional theory. We find that the reduction reaction is mainly governed by epoxide ring opening which is initiated by H transfer from hydrazine or its derivatives. In addition, our calculations suggest that the epoxide reduction by hydrazine may predominantly follow a direct Eley-Rideal mechanism rather than a Langmuir-Hinshelwood mechanism. We also discuss the generation of various hydrazine derivatives during the reduction of graphene oxide with hydrazine and their potential contribution to lowering the barrier height of epoxide ring opening.

Variational and perturbative formulations of quantum mechanical/molecular mechanical free energy with mean-field embedding and its analytical gradients.

PubMed

Yamamoto, Takeshi

2008-12-28

Conventional quantum chemical solvation theories are based on the mean-field embedding approximation. That is, the electronic wavefunction is calculated in the presence of the mean field of the environment. In this paper a direct quantum mechanical/molecular mechanical (QM/MM) analog of such a mean-field theory is formulated based on variational and perturbative frameworks. In the variational framework, an appropriate QM/MM free energy functional is defined and is minimized in terms of the trial wavefunction that best approximates the true QM wavefunction in a statistically averaged sense. Analytical free energy gradient is obtained, which takes the form of the gradient of effective QM energy calculated in the averaged MM potential. In the perturbative framework, the above variational procedure is shown to be equivalent to the first-order expansion of the QM energy (in the exact free energy expression) about the self-consistent reference field. This helps understand the relation between the variational procedure and the exact QM/MM free energy as well as existing QM/MM theories. Based on this, several ways are discussed for evaluating non-mean-field effects (i.e., statistical fluctuations of the QM wavefunction) that are neglected in the mean-field calculation. As an illustration, the method is applied to an S(N)2 Menshutkin reaction in water, NH(3)+CH(3)Cl-->NH(3)CH(3) (+)+Cl(-), for which free energy profiles are obtained at the Hartree-Fock, MP2, B3LYP, and BHHLYP levels by integrating the free energy gradient. Non-mean-field effects are evaluated to be <0.5 kcal/mol using a Gaussian fluctuation model for the environment, which suggests that those effects are rather small for the present reaction in water.

A comparison between semi-spheroid- and dome-shaped quantum dots coupled to wetting layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shahzadeh, Mohammadreza; Sabaeian, Mohammad, E-mail: Sabaeian@scu.ac.ir

2014-06-15

During the epitaxial growth method, self-assembled semi-spheroid-shaped quantum dots (QDs) are formed on the wetting layer (WL). However for sake of simplicity, researchers sometimes assume semi-spheroid-shaped QDs to be dome-shaped (hemisphere). In this work, a detailed and comprehensive study on the difference between electronic and transition properties of dome- and semi-spheroid-shaped quantum dots is presented. We will explain why the P-to-S intersubband transition behaves the way it does. The calculated results for intersubband P-to-S transition properties of quantum dots show two different trends for dome-shaped and semi-spheroid-shaped quantum dots. The results are interpreted using the probability of finding electron insidemore » the dome/spheroid region, with emphasis on the effects of wetting layer. It is shown that dome-shaped and semi-spheroid-shaped quantum dots feature different electronic and transition properties, arising from the difference in lateral dimensions between dome- and semi-spheroid-shaped QDs. Moreover, an analogy is presented between the bound S-states in the quantum dots and a simple 3D quantum mechanical particle in a box, and effective sizes are calculated. The results of this work will benefit researchers to present more realistic models of coupled QD/WL systems and explain their properties more precisely.« less

A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution.

PubMed

Lv, Jing; Zhang, Jingxue; Wang, Dunyou

2016-02-17

We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).

Influences of Quantum Mechanically Mixed Electronic and Vibrational Pigment States in 2D Electronic Spectra of Photosynthetic Systems: Strong Electronic Coupling Cases

DOE PAGES

Fujihashi, Yuta; Fleming, Graham R.; Ishizaki, Akihito

2015-09-07

In 2D electronic spectroscopy studies, long-lived quantum beats have recently been observed in photosynthetic systems, and several theoretical studies have suggested that the beats are produced by quantum mechanically mixed electronic and vibrational states. Concerning the electronic-vibrational quantum mixtures, the impact of protein-induced fluctuations was examined by calculating the 2D electronic spectra of a weakly coupled dimer with the Franck-Condon active vibrational modes in the resonant condition. This analysis demonstrated that quantum mixtures of the vibronic resonance are rather robust under the influence of the fluctuations at cryogenic temperatures, whereas the mixtures are eradicated by the fluctuations at physiological temperatures.more » However, this conclusion cannot be generalized because the magnitude of the coupling inducing the quantum mixtures is proportional to the inter-pigment electronic coupling. In this paper, we explore the impact of the fluctuations on electronic-vibrational quantum mixtures in a strongly coupled dimer with an off-resonant vibrational mode. Toward this end, we calculate energy transfer dynamics and 2D electronic spectra of a model dimer that corresponds to the most strongly coupled bacteriochlorophyll molecules in the Fenna-Matthews-Olson complex in a numerically accurate manner. The quantum mixtures are found to be robust under the exposure of protein-induced fluctuations at cryogenic temperatures, irrespective of the resonance. At 300 K, however, the quantum mixing is disturbed more strongly by the fluctuations, and therefore, the beats in the 2D spectra become obscure even in a strongly coupled dimer with a resonant vibrational mode. Further, the overall behaviors of the energy transfer dynamics are demonstrated to be dominated by the environment and coupling between the 0 0 vibronic transitions as long as the Huang-Rhys factor of the vibrational mode is small. Finally, the electronic-vibrational quantum mixtures do not necessarily play a significant role in electronic energy transfer dynamics despite contributing to the enhancement of long-lived quantum beating in the 2D spectra.« less

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Radiation of quantum black holes and modified uncertainty relation

NASA Astrophysics Data System (ADS)

Kamali, A. D.; Pedram, P.

In this paper, using a deformed algebra [X,P] = iℏ/(1 ‑ λ2P2) which is originated from various theories of gravity, we study thermodynamical properties of quantum black holes (BHs) in canonical ensembles. We exactly calculate the modified internal energy, entropy and heat capacity. Moreover, we investigate a tunneling mechanism of massless particle in phase space. In this regard, the tunneling radiation of BH receives new corrections and the exact radiant spectrum is no longer precisely thermal. In addition, we show that our results are compatible with other quantum gravity (QG) approaches.

A perspective on quantum mechanics calculations in ADMET predictions.

PubMed

Bowen, J Phillip; Güner, Osman F

2013-01-01

Understanding the molecular basis of drug action has been an important objective for pharmaceutical scientists. With the increasing speed of computers and the implementation of quantum chemistry methodologies, pharmacodynamic and pharmacokinetic problems have become more computationally tractable. Historically the former has been the focus of drug design, but within the last two decades efforts to understand the latter have increased. It takes about fifteen years and over $1 billion dollars for a drug to go from laboratory hit, through lead optimization, to final approval by the U.S. Food and Drug Administration. While the costs have increased substantially, the overall clinical success rate for a compound to emerge from clinical trials is approximately 10%. Most of the attrition rate can be traced to ADMET (absorption, distribution, metabolism, excretion, and toxicity) problems, which is a powerful impetus to study these issues at an earlier stage in drug discovery. Quantum mechanics offers pharmaceutical scientists the opportunity to investigate pharmacokinetic problems at the molecular level prior to laboratory preparation and testing. This review will provide a perspective on the use of quantum mechanics or a combination of quantum mechanics coupled with other classical methods in the pharmacokinetic phase of drug discovery. A brief overview of the essential features of theory will be discussed, and a few carefully selected examples will be given to highlight the computational methods.

Max Born and Molecular Theory

NASA Astrophysics Data System (ADS)

Rechenberg, H.

While the 20th century is approaching its conclusion, the historian may look back and assemble the essential scientific fruits of the this period. Nearly fifty years ago, Werner Heisenberg stated in a lecture that in quantum or wave mechanics ``a new, unified science of matter has arisen, where the separation between chemistry and physics essentially lost any meaning", because (Heisenberg 1953)``The chemical properties of atoms have at least in principle become accessible to calculation, and already in the first years after the rise of quantum mechanics the simplest chemical binding, namely that of the two hydrogen atoms in the hydrogen molecule was calculated with the help of the new methods and was found in closest agreement with chemical experience. Thus the chemical valency-forces were explained on a physical basis, and the application of the new knowledge in industrial practices became only a matter of time."

FT-Raman spectroscopy of the Candelaria and Pyxine lichen species: A new molecular structural study

NASA Astrophysics Data System (ADS)

Fernandes, Rafaella F.; Ferreira, Gilson R.; Spielmann, Adriano A.; Edwards, Howell G. M.; de Oliveira, Luiz Fernando C.

2015-12-01

In this work the chemistry of the lichens Candelaria fibrosa and Pyxine coccifera have been investigated for the first time using FT-Raman spectroscopy with the help of quantum mechanical DFT calculations to support spectral band assignments. The non-destructive spectral vibrational analysis provided evidence for the presence of pulvinic acid derivatives and conjugated polyenes, which probably belong to a carotenoid with characteristic signatures at ca. 1003, 1158 and 1525 cm-1 assigned respectively to δ(C-CH3), ν(C-C) and ν(Cdbnd C) modes. The identification of features arising from chiodectonic acid in the Pyxine species and calycin and pulvinic dilactone pigments in C. fibrosa were assisted by the quantum mechanical DFT calculations. Raman spectroscopy can provide important spectroscopic data for the identification of the biomarker spectral signatures nondestructively for these lichen pigments without the need for chemical extraction processes.

Retrieving plasmonic near-field information: A quantum-mechanical model for streaking photoelectron spectroscopy of gold nanospheres

NASA Astrophysics Data System (ADS)

Li, Jianxiong; Saydanzad, Erfan; Thumm, Uwe

2016-11-01

Streaked photoemission from nanostructures is characterized by size- and material-dependent nanometer-scale variations of the induced nanoplasmonic response to the electronic field of the streaking pulse and thus holds promise of allowing photoelectron imaging with both subfemtosecond temporal and nanometer spatial resolution. In order to scrutinize the driven collective electronic dynamics in 10-200-nm-diameter gold nanospheres, we calculated the plasmonic field induced by streaking pulses in the infrared and visible spectral range and developed a quantum-mechanical model for streaked photoemission by extreme ultraviolet pulses. Our simulated photoelectron spectra reveal a significant amplitude enhancement and phase shift of the photoelectron streaking trace relative to calculations that exclude the induced plasmonic field. Both are most pronounced for streaking pulses tuned to the plasmon frequency and retrace the plasmonic electromagnetic field enhancement and phase shift near the nanosphere surface.

Multi-fidelity machine learning models for accurate bandgap predictions of solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

Multi-fidelity machine learning models for accurate bandgap predictions of solids

DOE PAGES

Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

2016-12-28

Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

Investigation of the CH3Cl + CN(-) reaction in water: Multilevel quantum mechanics/molecular mechanics study.

PubMed

Xu, Yulong; Zhang, Jingxue; Wang, Dunyou

2015-06-28

The CH3Cl + CN(-) reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

Investigation of the CH3Cl + CN- reaction in water: Multilevel quantum mechanics/molecular mechanics study

NASA Astrophysics Data System (ADS)

Xu, Yulong; Zhang, Jingxue; Wang, Dunyou

2015-06-01

The CH3Cl + CN- reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack SN2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show that the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ˜11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

NASA Astrophysics Data System (ADS)

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

PubMed

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hao; Yang, Weitao, E-mail: weitao.yang@duke.edu; Department of Physics, Duke University, Durham, North Carolina 27708

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniformmore » external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics’ force fields and nontransferable molecule-specific atomic polarizabilities.« less

Rotational excitation of hydrogen molecules by collisions with hydrogen atoms. [interstellar gas energetics

NASA Technical Reports Server (NTRS)

Green, S.; Truhlar, D. G.

1979-01-01

Rate constants for rotational excitation of hydrogen molecules by collisions with hydrogen atoms have been obtained from quantum-mechanical calculations for kinetic temperatures between 100 and 5000 K. These calculations involve the rigid-rotator approximation, but other possible sources of error should be small. The calculations indicate that the early values of Nishimura are larger than accurate rigid-rotator values by about a factor of 20 or more.

On Mathematical Modeling Of Quantum Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Achuthan, P.; Dept. of Mathematics, Indian Institute of Technology, Madras, 600 036; Narayanankutty, Karuppath

2009-07-02

The world of physical systems at the most fundamental levels is replete with efficient, interesting models possessing sufficient ability to represent the reality to a considerable extent. So far, quantum mechanics (QM) forming the basis of almost all natural phenomena, has found beyond doubt its intrinsic ingenuity, capacity and robustness to stand the rigorous tests of validity from and through appropriate calculations and experiments. No serious failures of quantum mechanical predictions have been reported, yet. However, Albert Einstein, the greatest theoretical physicist of the twentieth century and some other eminent men of science have stated firmly and categorically that QM,more » though successful by and large, is incomplete. There are classical and quantum reality models including those based on consciousness. Relativistic quantum theoretical approaches to clearly understand the ultimate nature of matter as well as radiation have still much to accomplish in order to qualify for a final theory of everything (TOE). Mathematical models of better, suitable character as also strength are needed to achieve satisfactory explanation of natural processes and phenomena. We, in this paper, discuss some of these matters with certain apt illustrations as well.« less

Theoretical approaches for dynamical ordering of biomolecular systems.

PubMed

Okumura, Hisashi; Higashi, Masahiro; Yoshida, Yuichiro; Sato, Hirofumi; Akiyama, Ryo

2018-02-01

Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Methyl group dynamics in paracetamol and acetanilide: probing the static properties of intermolecular hydrogen bonds formed by peptide groups

NASA Astrophysics Data System (ADS)

Johnson, M. R.; Prager, M.; Grimm, H.; Neumann, M. A.; Kearley, G. J.; Wilson, C. C.

1999-06-01

Measurements of tunnelling and librational excitations for the methyl group in paracetamol and tunnelling excitations for the methyl group in acetanilide are reported. In both cases, results are compared with molecular mechanics calculations, based on the measured low temperature crystal structures, which follow an established recipe. Agreement between calculated and measured methyl group observables is not as good as expected and this is attributed to the presence of comprehensive hydrogen bond networks formed by the peptide groups. Good agreement is obtained with a periodic quantum chemistry calculation which uses density functional methods, these calculations confirming the validity of the one-dimensional rotational model used and the crystal structures. A correction to the Coulomb contribution to the rotational potential in the established recipe using semi-emipircal quantum chemistry methods, which accommodates the modified charge distribution due to the hydrogen bonds, is investigated.

Hybrid quantum-classical modeling of quantum dot devices

NASA Astrophysics Data System (ADS)

Kantner, Markus; Mittnenzweig, Markus; Koprucki, Thomas

2017-11-01

The design of electrically driven quantum dot devices for quantum optical applications asks for modeling approaches combining classical device physics with quantum mechanics. We connect the well-established fields of semiclassical semiconductor transport theory and the theory of open quantum systems to meet this requirement. By coupling the van Roosbroeck system with a quantum master equation in Lindblad form, we introduce a new hybrid quantum-classical modeling approach, which provides a comprehensive description of quantum dot devices on multiple scales: it enables the calculation of quantum optical figures of merit and the spatially resolved simulation of the current flow in realistic semiconductor device geometries in a unified way. We construct the interface between both theories in such a way, that the resulting hybrid system obeys the fundamental axioms of (non)equilibrium thermodynamics. We show that our approach guarantees the conservation of charge, consistency with the thermodynamic equilibrium and the second law of thermodynamics. The feasibility of the approach is demonstrated by numerical simulations of an electrically driven single-photon source based on a single quantum dot in the stationary and transient operation regime.

An Assessment of the Accuracy of Semi-Empirical Quantum Chemistry Calculations of the Mechanical Properties of Polymers

DTIC Science & Technology

1991-03-01

the crystal structure. The program Cerius 30 for Silicon Graphics workstations was used for this crystal simulation. A standard Lennard - Jones ...calculations ........... 16 2. General polymer stress-strain curve ......................... 23 3. Comparison of Morse and harmonic potentials ...a PE oligom er .......................................... 35 6. PE cluster strain dependent heat of formation potential ........... 36 7. Comparison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Özdemir, Semra Bayat; Demiralp, Metin

The determination of the energy states is highly studied issue in the quantum mechanics. Based on expectation values dynamics, energy states can be observed. But conditions and calculations vary depending on the created system. In this work, a symmetric exponential anharmonic oscillator is considered and development of a recursive approximation method is studied to find its ground energy state. The use of majorant values facilitates the approximate calculation of expectation values.

Spectroscopic (FT-IR, FT-Raman) and quantum mechanical studies of 3t-pentyl-2r,6c-diphenylpiperidin-4-one thiosemicarbazone

NASA Astrophysics Data System (ADS)

Savithiri, S.; Arockia doss, M.; Rajarajan, G.; Thanikachalam, V.; Bharanidharan, S.; Saleem, H.

2015-02-01

In this study, the molecular structure and vibrational spectra of 3t-pentyl2r,6c-diphenylpiperidin-4-one thiosemicarbazone (PDPOTSC) were studied. The ground-state molecular geometry was ascertained by using the density functional theory (DFT)/B3LYP method using 6-31++G(d,p) as a basis set. The vibrational (FT-IR and FT-Raman) spectra of PDPOTSC were computed using DFT/B3LYP and HF methods with 6-31++G(d,p) basis set. The fundamental vibrations were assigned on the basis of the total energy distribution (TED ⩾ 10%) of the vibrational modes, calculated with scaled quantum mechanics (SQM) methods PQS program. The electrical dipole moment (μ) and first hyperpolarizability (βo) values have been computed using DFT/B3LYP and HF methods. The calculated result (βo) shows that the title molecule might have nonlinear optical (NLO) behavior. Atomic charges of C, N, S and molecular electrostatic potential (MEP) were calculated using B3LYP/6-31G++(d,p). The HOMO-LUMO energies were calculated and natural bonding orbital (NBO) analysis has also been carried out.

Preface: Special Topic: From Quantum Mechanics to Force Fields.

PubMed

Piquemal, Jean-Philip; Jordan, Kenneth D

2017-10-28

This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

Preface: Special Topic: From Quantum Mechanics to Force Fields

NASA Astrophysics Data System (ADS)

Piquemal, Jean-Philip; Jordan, Kenneth D.

2017-10-01

This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

Non-adiabatic molecular dynamics with complex quantum trajectories. I. The diabatic representation.

PubMed

Zamstein, Noa; Tannor, David J

2012-12-14

We extend a recently developed quantum trajectory method [Y. Goldfarb, I. Degani, and D. J. Tannor, J. Chem. Phys. 125, 231103 (2006)] to treat non-adiabatic transitions. Each trajectory evolves on a single surface according to Newton's laws with complex positions and momenta. The transfer of amplitude between surfaces stems naturally from the equations of motion, without the need for surface hopping. In this paper we derive the equations of motion and show results in the diabatic representation, which is rarely used in trajectory methods for calculating non-adiabatic dynamics. We apply our method to the first two benchmark models introduced by Tully [J. Chem. Phys. 93, 1061 (1990)]. Besides giving the probability branching ratios between the surfaces, the method also allows the reconstruction of the time-dependent wavepacket. Our results are in quantitative agreement with converged quantum mechanical calculations.

Quantum field-theoretical description of neutrino and neutral kaon oscillations

NASA Astrophysics Data System (ADS)

Volobuev, Igor P.

2018-05-01

It is shown that the neutrino and neutral kaon oscillation processes can be consistently described in quantum field theory using only plane waves of the mass eigenstates of neutrinos and neutral kaons. To this end, the standard perturbative S-matrix formalism is modified so that it can be used for calculating the amplitudes of the processes passing at finite distances and finite time intervals. The distance-dependent and time-dependent parts of the amplitudes of the neutrino and neutral kaon oscillation processes are calculated and the results turn out to be in accordance with those of the standard quantum mechanical description of these processes based on the notion of neutrino flavor states and neutral kaon states with definite strangeness. However, the physical picture of the phenomena changes radically: now, there are no oscillations of flavor or definite strangeness states, but, instead of it, there is interference of amplitudes due to different virtual mass eigenstates.

Phase Diagram of Hydrogen and a Hydrogen-Helium Mixture at Planetary Conditions by Quantum Monte Carlo Simulations

NASA Astrophysics Data System (ADS)

Mazzola, Guglielmo; Helled, Ravit; Sorella, Sandro

2018-01-01

Understanding planetary interiors is directly linked to our ability of simulating exotic quantum mechanical systems such as hydrogen (H) and hydrogen-helium (H-He) mixtures at high pressures and temperatures. Equation of state (EOS) tables based on density functional theory are commonly used by planetary scientists, although this method allows only for a qualitative description of the phase diagram. Here we report quantum Monte Carlo (QMC) molecular dynamics simulations of pure H and H-He mixture. We calculate the first QMC EOS at 6000 K for a H-He mixture of a protosolar composition, and show the crucial influence of He on the H metallization pressure. Our results can be used to calibrate other EOS calculations and are very timely given the accurate determination of Jupiter's gravitational field from the NASA Juno mission and the effort to determine its structure.

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).

Periodic Toda lattice in quantum mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsuyama, A.

The quantum mechanical periodic Toda lattice is studied by the direct diagonalization of the Hamiltonian. The eigenstates are classified according to the irreducible representations of the dihedral group D[sub N]. It is shown that Gutzwiller's quantization conditions are satisfied and they have a one-to-one correspondence to the irreducible representation of the D[sub N] group. The authors have also carried out the semiclassical quantization of the periodic Toda lattice by the EBK formulation. The eigenvalues of the semiclassical quantization have a one-to-one correspondence to the integer quantum numbers, and those quantum numbers also have a close relationship to the symmetry ofmore » the state. Numerical calculations have been done for N = 3, 4, 5, and 6 particle periodic Toda lattices. The distributions of the eigenvalues are systematic and distinguished by the symmetry of the state. As illustrative examples, amplitudes of the wave functions and density distributions are shown. 14 refs., 8 figs., 11 tabs.« less

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

Electric dipole moments of the fluorescent probes Prodan and Laurdan: experimental and theoretical evaluations.

PubMed

Vequi-Suplicy, Cíntia C; Coutinho, Kaline; Lamy, M Teresa

2014-03-01

Several experimental and theoretical approaches can be used for a comprehensive understanding of solvent effects on the electronic structure of solutes. In this review, we revisit the influence of solvents on the electronic structure of the fluorescent probes Prodan and Laurdan, focusing on their electric dipole moments. These biologically used probes were synthesized to be sensitive to the environment polarity. However, their solvent-dependent electronic structures are still a matter of discussion in the literature. The absorption and emission spectra of Prodan and Laurdan in different solvents indicate that the two probes have very similar electronic structures in both the ground and excited states. Theoretical calculations confirm that their electronic ground states are very much alike. In this review, we discuss the electric dipole moments of the ground and excited states calculated using the widely applied Lippert-Mataga equation, using both spherical and spheroid prolate cavities for the solute. The dimensions of the cavity were found to be crucial for the calculated dipole moments. These values are compared to those obtained by quantum mechanics calculations, considering Prodan in vacuum, in a polarizable continuum solvent, and using a hybrid quantum mechanics-molecular mechanics methodology. Based on the theoretical approaches it is evident that the Prodan dipole moment can change even in the absence of solute-solvent-specific interactions, which is not taken into consideration with the experimental Lippert-Mataga method. Moreover, in water, for electric dipole moment calculations, it is fundamental to consider hydrogen-bonded molecules.

All-Dimensional H2–CO Potential: Validation with Fully Quantum Second Virial Coefficients

PubMed Central

Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H.

2017-01-01

We use a new high-accuracy all-dimensional potential to compute the cross second virial coefficient B12(T) between molecular hydrogen and carbon monoxide. The path-integral method is used to fully account for quantum effects. Values are calculated from 10 K to 2000 K and the uncertainty of the potential is propagated into uncertainties of B12. Our calculated B12(T) are in excellent agreement with most of the limited experimental data available, but cover a much wider range of temperatures and have lower uncertainties. Similar to recently reported findings from scattering calculations, we find that the reduced-dimensionality potential obtained by averaging over the rovibrational motion of the monomers gives results that are a good approximation to those obtained when flexibility is fully taken into account. Also, the four-dimensional approximation with monomers taken at their vibrationally averaged bond lengths works well. This finding is important, since full-dimensional potentials are difficult to develop even for triatomic monomers and are not currently possible to obtain for larger molecules. Likewise, most types of accurate quantum mechanical calculations, e.g., spectral or scattering, are severely limited in the number of dimensions that can be handled. PMID:28178790

All-dimensional H2-CO potential: Validation with fully quantum second virial coefficients.

PubMed

Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H

2017-02-07

We use a new high-accuracy all-dimensional potential to compute the cross second virial coefficient B 12 (T) between molecular hydrogen and carbon monoxide. The path-integral method is used to fully account for quantum effects. Values are calculated from 10 K to 2000 K and the uncertainty of the potential is propagated into uncertainties of B 12 . Our calculated B 12 (T) are in excellent agreement with most of the limited experimental data available, but cover a much wider range of temperatures and have lower uncertainties. Similar to recently reported findings from scattering calculations, we find that the reduced-dimensionality potential obtained by averaging over the rovibrational motion of the monomers gives results that are a good approximation to those obtained when flexibility is fully taken into account. Also, the four-dimensional approximation with monomers taken at their vibrationally averaged bond lengths works well. This finding is important, since full-dimensional potentials are difficult to develop even for triatomic monomers and are not currently possible to obtain for larger molecules. Likewise, most types of accurate quantum mechanical calculations, e.g., spectral or scattering, are severely limited in the number of dimensions that can be handled.

Reduced-Dimensionality Semiclassical Transition State Theory: Application to Hydrogen Atom Abstraction and Exchange Reactions of Hydrocarbons.

PubMed

Greene, Samuel M; Shan, Xiao; Clary, David C

2015-12-17

Quantum mechanical methods for calculating rate constants are often intractable for reactions involving many atoms. Semiclassical transition state theory (SCTST) offers computational advantages over these methods but nonetheless scales exponentially with the number of degrees of freedom (DOFs) of the system. Here we present a method with more favorable scaling, reduced-dimensionality SCTST (RD SCTST), that treats only a subset of DOFs of the system explicitly. We apply it to three H abstraction and exchange reactions for which two-dimensional potential energy surfaces (PESs) have previously been constructed and evaluated using RD quantum scattering calculations. We differentiated these PESs to calculate harmonic frequencies and anharmonic constants, which were then used to calculate cumulative reaction probabilities and rate constants by RD SCTST. This method yielded rate constants in good agreement with quantum scattering results. Notably, it performed well for a heavy-light-heavy reaction, even though it does not explicitly account for corner-cutting effects. Recent extensions to SCTST that improve its treatment of deep tunneling were also evaluated within the reduced-dimensionality framework. The success of RD SCTST in this study suggests its potential applicability to larger systems.

Energetic factors determining the binding of type I inhibitors to c-Met kinase: experimental studies and quantum mechanical calculations

PubMed Central

Yu, Zhe; Ma, Yu-chi; Ai, Jing; Chen, Dan-qi; Zhao, Dong-mei; Wang, Xin; Chen, Yue-lei; Geng, Mei-yu; Xiong, Bing; Cheng, Mao-sheng; Shen, Jing-kang

2013-01-01

Aim: To decipher the molecular interactions between c-Met and its type I inhibitors and to facilitate the design of novel c-Met inhibitors. Methods: Based on the prototype model inhibitor 1, four ligands with subtle differences in the fused aromatic rings were synthesized. Quantum chemistry was employed to calculate the binding free energy for each ligand. Symmetry-adapted perturbation theory (SAPT) was used to decompose the binding energy into several fundamental forces to elucidate the determinant factors. Results: Binding free energies calculated from quantum chemistry were correlated well with experimental data. SAPT calculations showed that the predominant driving force for binding was derived from a sandwich π–π interaction with Tyr-1230. Arg-1208 was the differentiating factor, interacting with the 6-position of the fused aromatic ring system through the backbone carbonyl with a force pattern similar to hydrogen bonding. Therefore, a hydrogen atom must be attached at the 6-position, and changing the carbon atom to nitrogen caused unfavorable electrostatic interactions. Conclusion: The theoretical studies have elucidated the determinant factors involved in the binding of type I inhibitors to c-Met. PMID:24056705

Linear free energy relationships between aqueous phase hydroxyl radical reaction rate constants and free energy of activation.

PubMed

Minakata, Daisuke; Crittenden, John

2011-04-15

The hydroxyl radical (HO(•)) is a strong oxidant that reacts with electron-rich sites on organic compounds and initiates complex radical chain reactions in aqueous phase advanced oxidation processes (AOPs). Computer based kinetic modeling requires a reaction pathway generator and predictions of associated reaction rate constants. Previously, we reported a reaction pathway generator that can enumerate the most important elementary reactions for aliphatic compounds. For the reaction rate constant predictor, we develop linear free energy relationships (LFERs) between aqueous phase literature-reported HO(•) reaction rate constants and theoretically calculated free energies of activation for H-atom abstraction from a C-H bond and HO(•) addition to alkenes. The theoretical method uses ab initio quantum mechanical calculations, Gaussian 1-3, for gas phase reactions and a solvation method, COSMO-RS theory, to estimate the impact of water. Theoretically calculated free energies of activation are found to be within approximately ±3 kcal/mol of experimental values. Considering errors that arise from quantum mechanical calculations and experiments, this should be within the acceptable errors. The established LFERs are used to predict the HO(•) reaction rate constants within a factor of 5 from the experimental values. This approach may be applied to other reaction mechanisms to establish a library of rate constant predictions for kinetic modeling of AOPs.

Dislocation-driven growth of two-dimensional lateral quantum-well superlattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Wu; Zhang, Yu -Yang; Chen, Jianyi

Here, the advent of two-dimensional (2D) materials has led to extensive studies of heterostructures for novel applications. 2D lateral multiheterojunctions and superlattices have been recently demonstrated, but the available growth methods can only produce features with widths in the micrometer or, at best, 100-nm scale and usually result in rough and defective interfaces with extensive chemical intermixing. Widths smaller than 5 nm, which are needed for quantum confinement effects and quantum-well applications, have not been achieved. We demonstrate the growth of sub–2-nm quantum-well arrays in semiconductor monolayers, driven by the climb of misfit dislocations in a lattice-mismatched sulfide/selenide heterointerface. Densitymore » functional theory calculations provide an atom-by-atom description of the growth mechanism. The calculated energy bands reveal type II alignment suitable for quantum wells, suggesting that the structure could, in principle, be turned into a “conduit” of conductive nanoribbons for interconnects in future 2D integrated circuits via n-type modulation doping. This misfit dislocation–driven growth can be applied to different combinations of 2D monolayers with lattice mismatch, paving the way to a wide range of 2D quantum-well superlattices with controllable band alignment and nanoscale width.« less

Dislocation-driven growth of two-dimensional lateral quantum-well superlattices

DOE PAGES

Zhou, Wu; Zhang, Yu -Yang; Chen, Jianyi; ...

2018-03-23

Here, the advent of two-dimensional (2D) materials has led to extensive studies of heterostructures for novel applications. 2D lateral multiheterojunctions and superlattices have been recently demonstrated, but the available growth methods can only produce features with widths in the micrometer or, at best, 100-nm scale and usually result in rough and defective interfaces with extensive chemical intermixing. Widths smaller than 5 nm, which are needed for quantum confinement effects and quantum-well applications, have not been achieved. We demonstrate the growth of sub–2-nm quantum-well arrays in semiconductor monolayers, driven by the climb of misfit dislocations in a lattice-mismatched sulfide/selenide heterointerface. Densitymore » functional theory calculations provide an atom-by-atom description of the growth mechanism. The calculated energy bands reveal type II alignment suitable for quantum wells, suggesting that the structure could, in principle, be turned into a “conduit” of conductive nanoribbons for interconnects in future 2D integrated circuits via n-type modulation doping. This misfit dislocation–driven growth can be applied to different combinations of 2D monolayers with lattice mismatch, paving the way to a wide range of 2D quantum-well superlattices with controllable band alignment and nanoscale width.« less

Increasing the efficiency and accuracy of time-resolved electronic spectra calculations with on-the-fly ab initio quantum dynamics methods

NASA Astrophysics Data System (ADS)

Vanicek, Jiri

2014-03-01

Rigorous quantum-mechanical calculations of coherent ultrafast electronic spectra remain difficult. I will present several approaches developed in our group that increase the efficiency and accuracy of such calculations: First, we justified the feasibility of evaluating time-resolved spectra of large systems by proving that the number of trajectories needed for convergence of the semiclassical dephasing representation/phase averaging is independent of dimensionality. Recently, we further accelerated this approximation with a cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. The accuracy of potential energy surfaces was increased by combining the dephasing representation with accurate on-the-fly ab initio electronic structure calculations, including nonadiabatic and spin-orbit couplings. Finally, the inherent semiclassical approximation was removed in the exact quantum Gaussian dephasing representation, in which semiclassical trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. Among other examples I will present an on-the-fly ab initio semiclassical dynamics calculation of the dispersed time-resolved stimulated emission spectrum of the 54-dimensional azulene. This research was supported by EPFL and by the Swiss National Science Foundation NCCR MUST (Molecular Ultrafast Science and Technology) and Grant No. 200021124936/1.

Mechanism of Microwave-Assisted Pyrolysis of Glucose to Furfural Revealed by Isotopic Tracer and Quantum Chemical Calculations.

PubMed

Bao, Liwei; Shi, Lei; Luo, Hu; Kong, Lingzhao; Li, Shenggang; Wei, Wei; Sun, Yuhan

2017-08-10

Glucose labeled with 13 C or 18 O was used to investigate the mechanism of its conversion into furfural by microwaveassisted pyrolysis. The isotopic content and location in furfural were determined from GC-MS and 13 C NMR spectroscopic measurements and data analysis. The results suggest that the carbon skeleton in furfural is mainly derived from C1 to C5 of glucose, whereas the C of the aldehyde group and the O of the furan ring in furfural primarily originate from C1 and O5 of glucose, respectively. For the first time, the source of O in the furan ring of furfural was elucidated directly by experiment, providing results that are consistent with predictions from recent quantum chemical calculations. Moreover, further theoretical calculations indicate substantially lower energy barriers than previous predictions by considering the potential catalytic effect of formic acid, which is one of the pyrolysis products. The catalytic role of formic acid is further confirmed by experimental evidence. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photodissociation dynamics in the first absorption band of pyrrole. II. Photofragment distributions for the 1A2(π σ* ) ←X˜ 1A1(π π ) transition

NASA Astrophysics Data System (ADS)

Picconi, David; Grebenshchikov, Sergy Yu.

2018-03-01

The analysis of the total kinetic energy release (TKER) of the photofragments pyrrolyl + H-atom formed in the photodissociation of pyrrole in the low-lying state 1A2(πσ*) is presented. The TKER distributions contain complementary and often more precise information on the fragmentation process than the broad diffuse absorption spectra. The distributions are calculated quantum mechanically for the diabatic state 1A2(πσ*) either isolated or coupled to the ground electronic state at an exit channel conical intersection. The calculations use the novel ab initio quasi-diabatic potential energy matrix constructed in the work of Picconi and Grebenshchikov [J. Chem. Phys. 148, 104103 (2018)]. The approximate overlap integral-based adiabatic mapping approach is introduced with which the quantum mechanical TKER distributions can be efficiently and accurately reproduced. Finally, the calculated TKERs are compared with the experimental results. The main features of the measured vibrationally resolved distributions are reproduced, and the spectral peaks are assigned and interpreted in detail.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

PubMed Central

Reimers, Jeffrey R.; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J.; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J. J.; Hendriksen, Bas L. M.; Elemans, Johannes A. A. W.; Hush, Noel S.; Crossley, Maxwell J.

2015-01-01

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate−molecule interactions (e.g., −100 kcal mol−1 to −150 kcal mol−1 for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70–110 kcal mol−1) and entropy effects (25–40 kcal mol−1 at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations. PMID:26512115

Applications and assessment of QM:QM electronic embedding using generalized asymmetric Mulliken atomic charges.

PubMed

Parandekar, Priya V; Hratchian, Hrant P; Raghavachari, Krishnan

2008-10-14

Hybrid QM:QM (quantum mechanics:quantum mechanics) and QM:MM (quantum mechanics:molecular mechanics) methods are widely used to calculate the electronic structure of large systems where a full quantum mechanical treatment at a desired high level of theory is computationally prohibitive. The ONIOM (our own N-layer integrated molecular orbital molecular mechanics) approximation is one of the more popular hybrid methods, where the total molecular system is divided into multiple layers, each treated at a different level of theory. In a previous publication, we developed a novel QM:QM electronic embedding scheme within the ONIOM framework, where the model system is embedded in the external Mulliken point charges of the surrounding low-level region to account for the polarization of the model system wave function. Therein, we derived and implemented a rigorous expression for the embedding energy as well as analytic gradients that depend on the derivatives of the external Mulliken point charges. In this work, we demonstrate the applicability of our QM:QM method with point charge embedding and assess its accuracy. We study two challenging systems--zinc metalloenzymes and silicon oxide cages--and demonstrate that electronic embedding shows significant improvement over mechanical embedding. We also develop a modified technique for the energy and analytic gradients using a generalized asymmetric Mulliken embedding method involving an unequal splitting of the Mulliken overlap populations to offer improvement in situations where the Mulliken charges may be deficient.

Two-photon processes based on quantum commutators

NASA Astrophysics Data System (ADS)

Fratini, F.; Safari, L.; Amaro, P.; Santos, J. P.

2018-04-01

We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed.

Electric dipole spin resonance in a quantum spin dimer system driven by magnetoelectric coupling

NASA Astrophysics Data System (ADS)

Kimura, Shojiro; Matsumoto, Masashige; Akaki, Mitsuru; Hagiwara, Masayuki; Kindo, Koichi; Tanaka, Hidekazu

2018-04-01

In this Rapid Communication, we propose a mechanism for electric dipole active spin resonance caused by spin-dependent electric polarization in a quantum spin gapped system. This proposal was successfully confirmed by high-frequency electron spin resonance (ESR) measurements of the quantum spin dimer system KCuCl3. ESR measurements by an illuminating linearly polarized electromagnetic wave reveal that the optical transition between the singlet and triplet states in KCuCl3 is driven by an ac electric field. The selection rule of the observed transition agrees with the calculation by taking into account spin-dependent electric polarization. We suggest that spin-dependent electric polarization is effective in achieving fast control of quantum spins by an ac electric field.

Dielectric properties of classical and quantized ionic fluids.

PubMed

Høye, Johan S

2010-06-01

We study time-dependent correlation functions of classical and quantum gases using methods of equilibrium statistical mechanics for systems of uniform as well as nonuniform densities. The basis for our approach is the path integral formalism of quantum mechanical systems. With this approach the statistical mechanics of a quantum mechanical system becomes the equivalent of a classical polymer problem in four dimensions where imaginary time is the fourth dimension. Several nontrivial results for quantum systems have been obtained earlier by this analogy. Here, we will focus upon the presence of a time-dependent electromagnetic pair interaction where the electromagnetic vector potential that depends upon currents, will be present. Thus both density and current correlations are needed to evaluate the influence of this interaction. Then we utilize that densities and currents can be expressed by polarizations by which the ionic fluid can be regarded as a dielectric one for which a nonlocal susceptibility is found. This nonlocality has as a consequence that we find no contribution from a possible transverse electric zero-frequency mode for the Casimir force between metallic plates. Further, we establish expressions for a leading correction to ab initio calculations for the energies of the quantized electrons of molecules where now retardation effects also are taken into account.

Numerical simulations in stochastic mechanics

NASA Astrophysics Data System (ADS)

McClendon, Marvin; Rabitz, Herschel

1988-05-01

The stochastic differential equation of Nelson's stochastic mechanics is integrated numerically for several simple quantum systems. The calculations are performed with use of Helfand and Greenside's method and pseudorandom numbers. The resulting trajectories are analyzed both individually and collectively to yield insight into momentum, uncertainty principles, interference, tunneling, quantum chaos, and common models of diatomic molecules from the stochastic quantization point of view. In addition to confirming Shucker's momentum theorem, these simulations illustrate, within the context of stochastic mechanics, the position-momentum and time-energy uncertainty relations, the two-slit diffraction pattern, exponential decay of an unstable system, and the greater degree of anticorrelation in a valence-bond model as compared with a molecular-orbital model of H2. The attempt to find exponential divergence of initially nearby trajectories, potentially useful as a criterion for quantum chaos, in a periodically forced oscillator is inconclusive. A way of computing excited energies from the ground-state motion is presented. In all of these studies the use of particle trajectories allows a more insightful interpretation of physical phenomena than is possible within traditional wave mechanics.

The structure of carbon nanotubes formed of graphene layers L4-8, L5-7, L3-12, L4-6-12

NASA Astrophysics Data System (ADS)

Shapovalova, K. E.; Belenkov, E. A.

2017-11-01

We geometrically calculate the optimized structure of nanotubes based on the graphene layers, using the method of molecular mechanics MM+. It was found that only the nanotubes, based on the graphene layers L4-8, L5-7, L3-12, L4-6-12, have a cylindrical form. Calculations of the sublimation energy, carried out using the semi-empirical quantum-mechanic method PM3, show that energy increases with the increase of nanotube diameters.

Quantum/molecular mechanics study of firefly bioluminescence on luciferase oxidative conformation

NASA Astrophysics Data System (ADS)

Pinto da Silva, Luís; Esteves da Silva, Joaquim C. G.

2014-07-01

This is the first report of a computational study of the color tuning mechanism of firefly bioluminescence, using the oxidative conformation of luciferase. The results of these calculations demonstrated that the electrostatic field generated by luciferase is fundamental both for the emission shift and efficiency. Further calculations indicated that a shift in emission is achieved by modulating the energy, at different degrees, of the emissive and ground states. These differences in energy modulation will then lead to changes in the energy gap between the states.

Future in biomolecular computation

NASA Astrophysics Data System (ADS)

Wimmer, E.

1988-01-01

Large-scale computations for biomolecules are dominated by three levels of theory: rigorous quantum mechanical calculations for molecules with up to about 30 atoms, semi-empirical quantum mechanical calculations for systems with up to several hundred atoms, and force-field molecular dynamics studies of biomacromolecules with 10,000 atoms and more including surrounding solvent molecules. It can be anticipated that increased computational power will allow the treatment of larger systems of ever growing complexity. Due to the scaling of the computational requirements with increasing number of atoms, the force-field approaches will benefit the most from increased computational power. On the other hand, progress in methodologies such as density functional theory will enable us to treat larger systems on a fully quantum mechanical level and a combination of molecular dynamics and quantum mechanics can be envisioned. One of the greatest challenges in biomolecular computation is the protein folding problem. It is unclear at this point, if an approach with current methodologies will lead to a satisfactory answer or if unconventional, new approaches will be necessary. In any event, due to the complexity of biomolecular systems, a hierarchy of approaches will have to be established and used in order to capture the wide ranges of length-scales and time-scales involved in biological processes. In terms of hardware development, speed and power of computers will increase while the price/performance ratio will become more and more favorable. Parallelism can be anticipated to become an integral architectural feature in a range of computers. It is unclear at this point, how fast massively parallel systems will become easy enough to use so that new methodological developments can be pursued on such computers. Current trends show that distributed processing such as the combination of convenient graphics workstations and powerful general-purpose supercomputers will lead to a new style of computing in which the calculations are monitored and manipulated as they proceed. The combination of a numeric approach with artificial-intelligence approaches can be expected to open up entirely new possibilities. Ultimately, the most exciding aspect of the future in biomolecular computing will be the unexpected discoveries.

Quantum chemical study of a derivative of 3-substituted dithiocarbamic flavanone

NASA Astrophysics Data System (ADS)

Gosav, Steluta; Paduraru, Nicoleta; Maftei, Dan; Birsa, Mihail Lucian; Praisler, Mirela

2017-02-01

The aim of this work is to characterize a quite novel 3-dithiocarbamic flavonoid by vibrational spectroscopy in conjunction with Density Functional Theory (DFT) calculations. Quantum mechanics calculations of energies, geometries and vibrational wavenumbers in the ground state were carried out by using hybrid functional B3LYP with 6-311G(d,p) as basis set. The results indicate a remarkable agreement between the calculated molecular geometries, as well as vibrational frequencies, and the corresponding experimental data. In addition, a complete assignment of all the absorption bands present in the vibrational spectrum has been performed. In order to assess its chemical potential, quantum molecular descriptors characterizing the interactions between the 3-dithiocarbamic flavonoid and its biological receptors have been computed. The frontier molecular orbitals and the HOMO-LUMO energy gap have been used in order to explain the way in which the new molecule can interact with other species and to characterize its molecular chemical stability/reactivity. The molecular electrostatic potential (MEP) map, computed in order to identify the sites of the studied flavonoid that are most likely to interact with electrophilic and nucleophilic species, is discussed.

Role of the Active Site Guanine in the glmS Ribozyme Self-Cleavage Mechanism: Quantum Mechanical/Molecular Mechanical Free Energy Simulations

PubMed Central

2015-01-01

The glmS ribozyme catalyzes a self-cleavage reaction at the phosphodiester bond between residues A-1 and G1. This reaction is thought to occur by an acid–base mechanism involving the glucosamine-6-phosphate cofactor and G40 residue. Herein quantum mechanical/molecular mechanical free energy simulations and pKa calculations, as well as experimental measurements of the rate constant for self-cleavage, are utilized to elucidate the mechanism, particularly the role of G40. Our calculations suggest that an external base deprotonates either G40(N1) or possibly A-1(O2′), which would be followed by proton transfer from G40(N1) to A-1(O2′). After this initial deprotonation, A-1(O2′) starts attacking the phosphate as a hydroxyl group, which is hydrogen-bonded to deprotonated G40, concurrent with G40(N1) moving closer to the hydroxyl group and directing the in-line attack. Proton transfer from A-1(O2′) to G40 is concomitant with attack of the scissile phosphate, followed by the remainder of the cleavage reaction. A mechanism in which an external base does not participate, but rather the proton transfers from A-1(O2′) to a nonbridging oxygen during nucleophilic attack, was also considered but deemed to be less likely due to its higher effective free energy barrier. The calculated rate constant for the favored mechanism is in agreement with the experimental rate constant measured at biological Mg2+ ion concentration. According to these calculations, catalysis is optimal when G40 has an elevated pKa rather than a pKa shifted toward neutrality, although a balance among the pKa’s of A-1, G40, and the nonbridging oxygen is essential. These results have general implications, as the hammerhead, hairpin, and twister ribozymes have guanines at a similar position as G40. PMID:25526516

Catalytic mechanism of phenylacetone monooxygenases for non-native linear substrates.

PubMed

Carvalho, Alexandra T P; Dourado, Daniel F A R; Skvortsov, Timofey; de Abreu, Miguel; Ferguson, Lyndsey J; Quinn, Derek J; Moody, Thomas S; Huang, Meilan

2017-10-11

Phenylacetone monooxygenase (PAMO) is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenase family, and therefore it is an ideal candidate for the synthesis of industrially relevant compounds. However, its limited substrate scope has largely limited its industrial applications. In the present work, we provide, for the first time, the catalytic mechanism of PAMO for the native substrate phenylacetone as well as for a linear non-native substrate 2-octanone, using molecular dynamics simulations, quantum mechanics and quantum mechanics/molecular mechanics calculations. We provide a theoretical basis for the preference of the enzyme for the native aromatic substrate over non-native linear substrates. Our study provides fundamental atomic-level insights that can be employed in the rational engineering of PAMO for wide applications in industrial biocatalysis, in particular, in the biotransformation of long-chain aliphatic oils into potential biodiesels.

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

PubMed

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

A quantum dynamical study of the He++2He-->He2++He reaction

NASA Astrophysics Data System (ADS)

Xie, Junkai; Poirier, Bill; Gellene, Gregory I.

2003-11-01

The temperature dependent rate of the He++2He→He2++He three-body association reaction is studied using two complementary quantum dynamical models. Model I presumes a two-step, reverse Lindemann mechanism, where the intermediate energized complex, He2+*, is interpreted as the rotational resonance states of He2+. The energy and width of these resonances are determined via "exact" quantum calculation using highly accurate potential-energy curves. Model II uses an alternate quantum rate expression as the thermal average of the cumulative recombination probability, N(E). This microcanonical quantity is computed approximately, over the He2+ space only, with the third-body interaction modeled using a special type of absorbing potential. Because Model II implicitly incorporates both the two-step reverse Lindemann mechanism, and a one-step, reverse collision induced dissociation mechanism, the relative importance of the two formation mechanisms can be estimated by a comparison of the Model I and Model II results. For T<300 K, the reaction is found to be dominated by the two-step mechanism, and a formation rate in good agreement with the available experimental results is obtained with essentially no adjustable parameters in the theory. Interestingly, a nonmonotonic He2+ formation rate is observed, with a maximum identified near 25 K. This maximum is associated with just two reaction intermediate resonance states, the lowest energy states that can contribute significantly to the formation kinetics.

Quantum Information Science: An Update

NASA Astrophysics Data System (ADS)

Kwek, L. C.; Zen, Freddy P.

2016-08-01

It is now roughly thirty years since the incipient ideas on quantum information science was concretely formalized. Over the last three decades, there has been much development in this field, and at least one technology, namely devices for quantum cryptography, is now commercialized. Yet, the holy grail of a workable quantum computing machine still lies faraway at the horizon. In any case, it took nearly several centuries before the vacuum tubes were invented after the first mechanical calculating were constructed, and several decades later, for the transistor to bring the current computer technology to fruition. In this review, we provide a short survey of the current development and progress in quantum information science. It clearly does not do justice to the amount of work in the past thirty years. Nevertheless, despite the modest attempt, this review hopes to induce younger researchers into this exciting field.

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems.

PubMed

Send, Robert; Kaila, Ville R I; Sundholm, Dage

2011-06-07

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes. © 2011 American Institute of Physics

Quantum turbulence and correlations in Bose-Einstein condensate collisions

NASA Astrophysics Data System (ADS)

Norrie, A. A.; Ballagh, R. J.; Gardiner, C. W.

2006-04-01

We investigate numerically simulated collisions between experimentally realistic Bose-Einstein condensate wave packets, within a regime where highly populated scattering haloes are formed. The theoretical basis for this work is the truncated Wigner method, for which we present a detailed derivation, paying particular attention to its validity regime for colliding condensates. This paper is an extension of our previous Letter [A. A. Norrie, R. J. Ballagh, and C. W. Gardiner, Phys. Rev. Lett. 94, 040401 (2005)], and we investigate both single-trajectory solutions, which reveal the presence of quantum turbulence in the scattering halo, and ensembles of trajectories, which we use to calculate quantum-mechanical correlation functions of the field.

LETTER TO THE EDITOR: Quantum manifestations of closed orbits in the photoexcitation scaled spectrum of the hydrogen atom in crossed fields

NASA Astrophysics Data System (ADS)

Rao, Jianguo; Delande, D.; Taylor, K. T.

2001-06-01

The scaled photoexcitation spectrum of the hydrogen atom in crossed electric and magnetic fields has been obtained by means of accurate quantum mechanical calculation using a new algorithm. Closed orbits in the corresponding classical system have also been obtained, using a new, efficient and practical searching procedure. Two new classes of closed orbit have been identified. Fourier transforming each photoexcitation quantum spectrum to yield a plot against scaled action has allowed direct comparison between peaks in such plots and the scaled action values of closed orbits. Excellent agreement has been found with all peaks assigned.

Analysis of quantum error-correcting codes: Symplectic lattice codes and toric codes

NASA Astrophysics Data System (ADS)

Harrington, James William

Quantum information theory is concerned with identifying how quantum mechanical resources (such as entangled quantum states) can be utilized for a number of information processing tasks, including data storage, computation, communication, and cryptography. Efficient quantum algorithms and protocols have been developed for performing some tasks (e.g. , factoring large numbers, securely communicating over a public channel, and simulating quantum mechanical systems) that appear to be very difficult with just classical resources. In addition to identifying the separation between classical and quantum computational power, much of the theoretical focus in this field over the last decade has been concerned with finding novel ways of encoding quantum information that are robust against errors, which is an important step toward building practical quantum information processing devices. In this thesis I present some results on the quantum error-correcting properties of oscillator codes (also described as symplectic lattice codes) and toric codes. Any harmonic oscillator system (such as a mode of light) can be encoded with quantum information via symplectic lattice codes that are robust against shifts in the system's continuous quantum variables. I show the existence of lattice codes whose achievable rates match the one-shot coherent information over the Gaussian quantum channel. Also, I construct a family of symplectic self-dual lattices and search for optimal encodings of quantum information distributed between several oscillators. Toric codes provide encodings of quantum information into two-dimensional spin lattices that are robust against local clusters of errors and which require only local quantum operations for error correction. Numerical simulations of this system under various error models provide a calculation of the accuracy threshold for quantum memory using toric codes, which can be related to phase transitions in certain condensed matter models. I also present a local classical processing scheme for correcting errors on toric codes, which demonstrates that quantum information can be maintained in two dimensions by purely local (quantum and classical) resources.

Cryptographic robustness of practical quantum cryptography: BB84 key distribution protocol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Molotkov, S. N.

2008-07-15

In real fiber-optic quantum cryptography systems, the avalanche photodiodes are not perfect, the source of quantum states is not a single-photon one, and the communication channel is lossy. For these reasons, key distribution is impossible under certain conditions for the system parameters. A simple analysis is performed to find relations between the parameters of real cryptography systems and the length of the quantum channel that guarantee secure quantum key distribution when the eavesdropper's capabilities are limited only by fundamental laws of quantum mechanics while the devices employed by the legitimate users are based on current technologies. Critical values are determinedmore » for the rate of secure real-time key generation that can be reached under the current technology level. Calculations show that the upper bound on channel length can be as high as 300 km for imperfect photodetectors (avalanche photodiodes) with present-day quantum efficiency ({eta} {approx} 20%) and dark count probability (p{sub dark} {approx} 10{sup -7})« less

Cryptographic robustness of practical quantum cryptography: BB84 key distribution protocol

NASA Astrophysics Data System (ADS)

Molotkov, S. N.

2008-07-01

In real fiber-optic quantum cryptography systems, the avalanche photodiodes are not perfect, the source of quantum states is not a single-photon one, and the communication channel is lossy. For these reasons, key distribution is impossible under certain conditions for the system parameters. A simple analysis is performed to find relations between the parameters of real cryptography systems and the length of the quantum channel that guarantee secure quantum key distribution when the eavesdropper’s capabilities are limited only by fundamental laws of quantum mechanics while the devices employed by the legitimate users are based on current technologies. Critical values are determined for the rate of secure real-time key generation that can be reached under the current technology level. Calculations show that the upper bound on channel length can be as high as 300 km for imperfect photodetectors (avalanche photodiodes) with present-day quantum efficiency (η ≈ 20%) and dark count probability ( p dark ˜ 10-7).

Quantum-like dynamics of decision-making in prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu

2012-03-01

In cognitive psychology, some experiments of games were reported [1, 2, 3, 4], and these demonstrated that real players did not use the "rational strategy" provided by classical game theory. To discuss probabilities of such "irrational choice", recently, we proposed a decision-making model which is based on the formalism of quantum mechanics [5, 6, 7, 8]. In this paper, we briefly explain the above model and calculate the probability of irrational choice in several prisoner's dilemma (PD) games.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brezov, D. S.; Mladenova, C. D.; Mladenov, I. M., E-mail: mladenov@bio21.bas.bg

In this paper we obtain the Lie derivatives of the scalar parameters in the generalized Euler decomposition with respect to arbitrary axes under left and right deck transformations. This problem can be directly related to the representation of the angular momentum in quantum mechanics. As a particular example, we calculate the angular momentum and the corresponding quantum hamiltonian in the standard Euler and Bryan representations. Similarly, in the hyperbolic case, the Laplace-Beltrami operator is retrieved for the Iwasawa decomposition. The case of two axes is considered as well.

One-electron propagation in Fermi, Pasta, Ulam disordered chains with Gaussian acoustic pulse pumping

NASA Astrophysics Data System (ADS)

Silva, L. D. Da; Dos Santos, J. L. L.; Ranciaro Neto, A.; Sales, M. O.; de Moura, F. A. B. F.

In this work, we consider a one-electron moving on a Fermi, Pasta, Ulam disordered chain under effect of electron-phonon interaction and a Gaussian acoustic pulse pumping. We describe electronic dynamics using quantum mechanics formalism and the nonlinear atomic vibrations using standard classical physics. Solving numerical equations related to coupled quantum/classical behavior of this system, we study electronic propagation properties. Our calculations suggest that the acoustic pumping associated with the electron-lattice interaction promote a sub-diffusive electronic dynamics.

Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

PubMed

Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

2014-09-16

Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.

Annular tautomerism: experimental observations and quantum mechanics calculations.

PubMed

Cruz-Cabeza, Aurora J; Schreyer, Adrian; Pitt, William R

2010-06-01

The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein-small molecule crystal structures.

Annular tautomerism: experimental observations and quantum mechanics calculations

NASA Astrophysics Data System (ADS)

Cruz-Cabeza, Aurora J.; Schreyer, Adrian; Pitt, William R.

2010-06-01

The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein—small molecule crystal structures.

Induced Angular Momentum

ERIC Educational Resources Information Center

Parker, G. W.

1978-01-01

Discusses, classically and quantum mechanically, the angular momentum induced in the bound motion of an electron by an external magnetic field. Calculates the current density and its magnetic moment, and then uses two methods to solve the first-order perturbation theory equation for the required eigenfunction. (Author/GA)

First-principles quantum-mechanical investigations: The role of water in catalytic conversion of furfural on Pd(111)

NASA Astrophysics Data System (ADS)

Xue, Wenhua; Borja, Miguel Gonzalez; Resasco, Daniel E.; Wang, Sanwu

2015-03-01

In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of water has attracted wide attention. Recent experiments showed that the proportion of alcohol product from catalytic reactions of furfural conversion with palladium in the presence of water is significantly increased, when compared with other solvent including dioxane, decalin, and ethanol. We investigated the microscopic mechanism of the reactions based on first-principles quantum-mechanical calculations. We particularly identified the important role of water and the liquid/solid interface in furfural conversion. Our results provide atomic-scale details for the catalytic reactions. Supported by DOE (DE-SC0004600). This research used the supercomputer resources at NERSC, of XSEDE, at TACC, and at the Tandy Supercomputing Center.

Computed potential energy surfaces for chemical reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.

1994-01-01

Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mingda; Cui, Wenping; Dresselhaus, Mildred S.

Crystal dislocations govern the plastic mechanical properties of materials but also affect the electrical and optical properties. However, a fundamental and quantitative quantum field theory of a dislocation has remained undiscovered for decades. Here in this article we present an exactly-solvable one-dimensional quantum field theory of a dislocation, for both edge and screw dislocations in an isotropic medium, by introducing a new quasiparticle which we have called the ‘dislon’. The electron-dislocation relaxation time can then be studied directly from the electron self-energy calculation, which is reducible to classical results. In addition, we predict that the electron energy will experience anmore » oscillation pattern near a dislocation. Compared with the electron density’s Friedel oscillation, such an oscillation is intrinsically different since it exists even with only single electron is present. With our approach, the effect of dislocations on materials’ non-mechanical properties can be studied at a full quantum field theoretical level.« less

A Time-Space Symmetry Based Cylindrical Model for Quantum Mechanical Interpretations

NASA Astrophysics Data System (ADS)

Vo Van, Thuan

2017-12-01

Following a bi-cylindrical model of geometrical dynamics, our study shows that a 6D-gravitational equation leads to geodesic description in an extended symmetrical time-space, which fits Hubble-like expansion on a microscopic scale. As a duality, the geodesic solution is mathematically equivalent to the basic Klein-Gordon-Fock equations of free massive elementary particles, in particular, the squared Dirac equations of leptons. The quantum indeterminism is proved to have originated from space-time curvatures. Interpretation of some important issues of quantum mechanical reality is carried out in comparison with the 5D space-time-matter theory. A solution of lepton mass hierarchy is proposed by extending to higher dimensional curvatures of time-like hyper-spherical surfaces than one of the cylindrical dynamical geometry. In a result, the reasonable charged lepton mass ratios have been calculated, which would be tested experimentally.

Quantum Mechanical Approach to Understanding Structural, Electronic and Mechanical Properties of Intermetallics

DTIC Science & Technology

1989-01-26

Understanding Structural , Electronic and Mechanical Properties of Tntermetallics by A.J. Freeman, Principal Investigator ABSTRACT The primary goal of...like LI or Mg would lower EF into the minimum in the DOS and hence stabilize the L1 2 . A. Structural Phase Stability of Titanium Aluminides Most...34 Structural Stability Calculations in the Titanium -Aluminium System", Conf. on Titanium Aluminides , Wright-Patterson Air Force Base, Nov. 1986

Quantum Mechanical Study of γ-Fe2O3 Nanoparticle as a Nanocarrier for Anticancer Drug Delivery

NASA Astrophysics Data System (ADS)

Lari, Hadi; Morsali, Ali; Heravi, Mohammad Momen

2018-05-01

Using density functional theory (DFT), noncovalent interactions and four mechanisms of covalent functionalization of melphalan anticancer drug onto γ-Fe2O3 nanoparticles have been studied. Quantum molecular descriptors of noncovalent configurations were investigated. It was specified that binding of melphalan onto γ-Fe2O3 nanoparticles is thermodynamically suitable. Hardness and the gap of energy between LUMO and HOMO of melphalan are higher than the noncovalent configurations, showing the reactivity of drug increases in the presence of γ-Fe2O3 nanoparticles. Melphalan can bond to γ-Fe2O3 nanoparticles through NH2 (k1 mechanism), OH (k2 mechanism), C=O (k3 mechanism) and Cl (k4 mechanism) groups. The activation energies, the activation enthalpies and the activation Gibbs free energies of these reactions were calculated. Thermodynamic data indicate that k3 mechanism is exothermic and spontaneous and can take place at room temperature. These results could be generalized to other similar drugs.

Investigation of the CH{sub 3}Cl + CN{sup −} reaction in water: Multilevel quantum mechanics/molecular mechanics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Yulong; College of Physics and Electronics, Shandong Normal University, Jinan 250014; Zhang, Jingxue

2015-06-28

The CH{sub 3}Cl + CN{sup −} reaction in water was studied using a multilevel quantum mechanics/molecular mechanics (MM) method with the multilevels, electrostatic potential, density functional theory (DFT) and coupled-cluster single double triple (CCSD(T)), for the solute region. The detailed, back-side attack S{sub N}2 reaction mechanism was mapped along the reaction pathway. The potentials of mean force were calculated under both the DFT and CCSD(T) levels for the reaction region. The CCSD(T)/MM level of theory presents a free energy activation barrier height at 20.3 kcal/mol, which agrees very well with the experiment value at 21.6 kcal/mol. The results show thatmore » the aqueous solution has a dominant role in shaping the potential of mean force. The solvation effect and the polarization effect together increase the activation barrier height by ∼11.4 kcal/mol: the solvation effect plays a major role by providing about 75% of the contribution, while polarization effect only contributes 25% to the activation barrier height. Our calculated potential of mean force under the CCSD(T)/MM also has a good agreement with the one estimated using data from previous gas-phase studies.« less

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction.

PubMed

Sadowski, Peter; Fooshee, David; Subrahmanya, Niranjan; Baldi, Pierre

2016-11-28

Machine learning (ML) and quantum mechanical (QM) methods can be used in two-way synergy to build chemical reaction expert systems. The proposed ML approach identifies electron sources and sinks among reactants and then ranks all source-sink pairs. This addresses a bottleneck of QM calculations by providing a prioritized list of mechanistic reaction steps. QM modeling can then be used to compute the transition states and activation energies of the top-ranked reactions, providing additional or improved examples of ranked source-sink pairs. Retraining the ML model closes the loop, producing more accurate predictions from a larger training set. The approach is demonstrated in detail using a small set of organic radical reactions.

A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1.

PubMed

Zhu, Kongkai; Lu, Junyan; Liang, Zhongjie; Kong, Xiangqian; Ye, Fei; Jin, Lu; Geng, Heji; Chen, Yong; Zheng, Mingyue; Jiang, Hualiang; Li, Jun-Qian; Luo, Cheng

2013-03-01

New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a major global threat to human health for its rapid rate of dissemination and ability to make pathogenic microbes resistant to almost all known β-lactam antibiotics. In addition, effective NDM-1 inhibitors have not been identified to date. In spite of the plethora of structural and kinetic data available, the accurate molecular characteristics of and details on the enzymatic reaction of NDM-1 hydrolyzing β-lactam antibiotics remain incompletely understood. In this study, a combined computational approach including molecular docking, molecular dynamics simulations and quantum mechanics/molecular mechanics calculations was performed to characterize the catalytic mechanism of meropenem catalyzed by NDM-1. The quantum mechanics/molecular mechanics results indicate that the ionized D124 is beneficial to the cleavage of the C-N bond within the β-lactam ring. Meanwhile, it is energetically favorable to form an intermediate if no water molecule coordinates to Zn2. Moreover, according to the molecular dynamics results, the conserved residue K211 plays a pivotal role in substrate binding and catalysis, which is quite consistent with previous mutagenesis data. Our study provides detailed insights into the catalytic mechanism of NDM-1 hydrolyzing meropenem β-lactam antibiotics and offers clues for the discovery of new antibiotics against NDM-1 positive strains in clinical studies.

Resonant electronic excitation energy transfer by exchange mechanism in the quantum dot system

NASA Astrophysics Data System (ADS)

Chikalova-Luzina, O. P.; Samosvat, D. M.; Vyatkin, V. M.; Zegrya, G. G.

2017-11-01

A microscopic theory of nonradiative resonance energy transfer between spherical A3B5 semiconductor quantum dots by the exchange mechanism is suggested. The interdot Coulomb interaction is taken into consideration. It is assumed that the quantum dot-donor and the quantum dot-acceptor are made from the same A3B5 compound and are embedded in the matrix of another material that produces potential barriers for electrons and holes. The dependences of the energy transfer rate on the quantum-dot system parameters are found in the frame of the Kane model that provides the most adequate description of the real spectra of A3B5 semiconductors. The analytical treatment is carried out with using the density matrix method, which enabled us to perform an energy transfer analysis both in the weak-interaction approximation and in the strong-interaction approximation. The numerical calculations showed the saturation of the energy transfer rate at the distances between the donor and the acceptor approaching the contact one. The contributions of the exchange and direct Coulomb intractions can be of the same order at the small distances and can have the same value in the saturation range.

High-Level, First-Principles, Full-Dimensional Quantum Calculation of the Ro-vibrational Spectrum of the Simplest Criegee Intermediate (CH2OO).

PubMed

Li, Jun; Carter, Stuart; Bowman, Joel M; Dawes, Richard; Xie, Daiqian; Guo, Hua

2014-07-03

The ro-vibrational spectrum of the simplest Criegee intermediate (CH2OO) has been determined quantum mechanically based on nine-dimensional potential energy and dipole surfaces for its ground electronic state. The potential energy surface is fitted to more than 50 000 high-level ab initio points with a root-mean-square error of 25 cm(-1), using a recently proposed permutation invariant polynomial neural network method. The calculated rotational constants, vibrational frequencies, and spectral intensities of CH2OO are in excellent agreement with experiment. The potential energy surface provides a valuable platform for studying highly excited vibrational and unimolecular reaction dynamics of this important molecule.

The rate constant of a quantum-diffusion-controlled bimolecular reaction

NASA Astrophysics Data System (ADS)

Bondarev, B. V.

1986-04-01

A quantum-mechanical equation is derived in the tight-bond approximation which describes the motion and chemical interaction of a pair of species A and B when their displacement in the matrix is caused by tunnelling. Within the framework of the discrete model of random walks, definitions are given of the probability and rate constant of a reaction A + B → P (products) proceeding in a condensed medium. A method is suggested for calculating the rate constant of a quantum-diffusion-controlled bimolecular reaction. By this method, an expression is obtained for the rate constant in the stationary spherically symmetrical case. An equation for the density matrix is also proposed which describes the motion and chemical interaction of a pair of species when the quantum and classical diffusion are competitive.

Coulomb Mediated Hybridization of Excitons in Coupled Quantum Dots.

PubMed

Ardelt, P-L; Gawarecki, K; Müller, K; Waeber, A M; Bechtold, A; Oberhofer, K; Daniels, J M; Klotz, F; Bichler, M; Kuhn, T; Krenner, H J; Machnikowski, P; Finley, J J

2016-02-19

We report Coulomb mediated hybridization of excitonic states in optically active InGaAs quantum dot molecules. By probing the optical response of an individual quantum dot molecule as a function of the static electric field applied along the molecular axis, we observe unexpected avoided level crossings that do not arise from the dominant single-particle tunnel coupling. We identify a new few-particle coupling mechanism stemming from Coulomb interactions between different neutral exciton states. Such Coulomb resonances hybridize the exciton wave function over four different electron and hole single-particle orbitals. Comparisons of experimental observations with microscopic eight-band k·p calculations taking into account a realistic quantum dot geometry show good agreement and reveal that the Coulomb resonances arise from broken symmetry in the artificial semiconductor molecule.

Quantum and quasiclassical dynamics of the multi-channel H + H2S reaction.

PubMed

Qi, Ji; Lu, Dandan; Song, Hongwei; Li, Jun; Yang, Minghui

2017-03-28

The prototypical multi-channel reaction H + H 2 S → H 2 + SH/H + H 2 S has been investigated using the full-dimensional quantum scattering and quasi-classical trajectory methods to unveil the underlying competition mechanism between different product channels and the mode specificity. This reaction favors the abstraction channel over the exchange channel. For both channels, excitations in the two stretching modes promote the reaction with nearly equal efficiency and are more efficient than the bending mode excitation. However, they are all less efficient than the translational energy. In addition, the experimentally observed non-Arrhenius temperature dependence of the thermal rate constants is reasonably reproduced by the quantum dynamics calculations, confirming that the non-Arrhenius behavior is caused by the pronounced quantum tunneling.

Quantum random number generation for loophole-free Bell tests

NASA Astrophysics Data System (ADS)

Mitchell, Morgan; Abellan, Carlos; Amaya, Waldimar

2015-05-01

We describe the generation of quantum random numbers at multi-Gbps rates, combined with real-time randomness extraction, to give very high purity random numbers based on quantum events at most tens of ns in the past. The system satisfies the stringent requirements of quantum non-locality tests that aim to close the timing loophole. We describe the generation mechanism using spontaneous-emission-driven phase diffusion in a semiconductor laser, digitization, and extraction by parity calculation using multi-GHz logic chips. We pay special attention to experimental proof of the quality of the random numbers and analysis of the randomness extraction. In contrast to widely-used models of randomness generators in the computer science literature, we argue that randomness generation by spontaneous emission can be extracted from a single source.

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline L-alanine

NASA Astrophysics Data System (ADS)

Williams, Robert W.; Schlücker, Sebastian; Hudson, Bruce S.

2008-01-01

A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes.

Full-dimensional quantum mechanics calculations for the spectroscopic characterization of the isomerization transition states of HOCO/DOCO systems.

PubMed

Ma, Dandan; Ren, Haisheng; Ma, Jianyi

2018-02-14

Full-dimensional quantum mechanics calculations were performed to determine the vibrational energy levels of HOCO and DOCO based on an accurate potential energy surface. Almost all of the vibrational energy levels up to 3500 cm -1 from the vibrational ground state were assigned, and the calculated energy levels in this work are well in agreement with the reported results by Bowman. The corresponding full dimensional wavefunctions present some special features. When the energy level approaches the barrier height, the trans-HOCO and cis-HOCO states strongly couple through tunneling interactions, and the tunneling interaction and Fermi resonance were observed in the DOCO system. The energy level patterns of trans-HOCO, cis-HOCO and trans-DOCO provide a reasonable fitted barrier height using the fitting formula of Field et al., however, a discrepancy exists for the cis-DOCO species which is considered as a random event. Our full-dimensional calculations give positive evidence for the accuracy of the spectroscopic characterization model of the isomerization transition state reported by Field et al., which was developed from one-dimensional model systems. Furthermore, the special case of cis-DOCO in this work means that the isotopic substitution can solve the problem of the accidental failure of Field's spectroscopic characterization model.

Excited-state relaxation in PbSe quantum dots

NASA Astrophysics Data System (ADS)

An, Joonhee M.; Califano, Marco; Franceschetti, Alberto; Zunger, Alex

2008-04-01

In solids the phonon-assisted, nonradiative decay from high-energy electronic excited states to low-energy electronic excited states is picosecond fast. It was hoped that electron and hole relaxation could be slowed down in quantum dots, due to the unavailability of phonons energy matched to the large energy-level spacings ("phonon-bottleneck"). However, excited-state relaxation was observed to be rather fast (⩽1ps) in InP, CdSe, and ZnO dots, and explained by an efficient Auger mechanism, whereby the excess energy of electrons is nonradiatively transferred to holes, which can then rapidly decay by phonon emission, by virtue of the densely spaced valence-band levels. The recent emergence of PbSe as a novel quantum-dot material has rekindled the hope for a slow down of excited-state relaxation because hole relaxation was deemed to be ineffective on account of the widely spaced hole levels. The assumption of sparse hole energy levels in PbSe was based on an effective-mass argument based on the light effective mass of the hole. Surprisingly, fast intraband relaxation times of 1-7ps were observed in PbSe quantum dots and have been considered contradictory with the Auger cooling mechanism because of the assumed sparsity of the hole energy levels. Our pseudopotential calculations, however, do not support the scenario of sparse hole levels in PbSe: Because of the existence of three valence-band maxima in the bulk PbSe band structure, hole energy levels are densely spaced, in contradiction with simple effective-mass models. The remaining question is whether the Auger decay channel is sufficiently fast to account for the fast intraband relaxation. Using the atomistic pseudopotential wave functions of Pb2046Se2117 and Pb260Se249 quantum dots, we explicitly calculated the electron-hole Coulomb integrals and the P →S electron Auger relaxation rate. We find that the Auger mechanism can explain the experimentally observed P →S intraband decay time scale without the need to invoke any exotic relaxation mechanisms.

The quantum Zeno effect in double well tunnelling

NASA Astrophysics Data System (ADS)

Lerner, L.

2018-05-01

Measurement lies at the heart of quantum theory, and introductory textbooks in quantum mechanics cover the measurement problem in topics such as the Schrödinger’s cat thought experiment, the EPR problem, and the quantum Zeno effect (QZE). In this article we present a new treatment of the QZE suitable for undergraduate students, for the case of a particle tunnelling between two wells while being observed in one of the wells. The analysis shows that as the observation rate increases, the tunnelling rate tends towards zero, in accordance with Zeno’s maxim ‘a watched pot never boils’. The method relies on decoherence theory, which replaces aspects of quantum collapse by the Schrödinger evolution of an open system, and its recently simplified treatment for undergraduates. Our presentation uses concepts familiar to undergraduate students, so that calculations involving many-body theory and the formal properties of the density matrix are avoided.

Quantum computing with defects.

PubMed

Weber, J R; Koehl, W F; Varley, J B; Janotti, A; Buckley, B B; Van de Walle, C G; Awschalom, D D

2010-05-11

Identifying and designing physical systems for use as qubits, the basic units of quantum information, are critical steps in the development of a quantum computer. Among the possibilities in the solid state, a defect in diamond known as the nitrogen-vacancy (NV(-1)) center stands out for its robustness--its quantum state can be initialized, manipulated, and measured with high fidelity at room temperature. Here we describe how to systematically identify other deep center defects with similar quantum-mechanical properties. We present a list of physical criteria that these centers and their hosts should meet and explain how these requirements can be used in conjunction with electronic structure theory to intelligently sort through candidate defect systems. To illustrate these points in detail, we compare electronic structure calculations of the NV(-1) center in diamond with those of several deep centers in 4H silicon carbide (SiC). We then discuss the proposed criteria for similar defects in other tetrahedrally coordinated semiconductors.

Frictional lubricity enhanced by quantum mechanics.

PubMed

Zanca, Tommaso; Pellegrini, Franco; Santoro, Giuseppe E; Tosatti, Erio

2018-04-03

The quantum motion of nuclei, generally ignored in the physics of sliding friction, can affect in an important manner the frictional dissipation of a light particle forced to slide in an optical lattice. The density matrix-calculated evolution of the quantum version of the basic Prandtl-Tomlinson model, describing the dragging by an external force of a point particle in a periodic potential, shows that purely classical friction predictions can be very wrong. The strongest quantum effect occurs not for weak but for strong periodic potentials, where barriers are high but energy levels in each well are discrete, and resonant Rabi or Landau-Zener tunneling to states in the nearest well can preempt classical stick-slip with nonnegligible efficiency, depending on the forcing speed. The resulting permeation of otherwise unsurmountable barriers is predicted to cause quantum lubricity, a phenomenon which we expect should be observable in the recently implemented sliding cold ion experiments.

Quantum-statistical theory of microwave detection using superconducting tunnel junctions

NASA Astrophysics Data System (ADS)

Deviatov, I. A.; Kuzmin, L. S.; Likharev, K. K.; Migulin, V. V.; Zorin, A. B.

1986-09-01

A quantum-statistical theory of microwave and millimeter-wave detection using superconducting tunnel junctions is developed, with a rigorous account of quantum, thermal, and shot noise arising from fluctuation sources associated with the junctions, signal source, and matching circuits. The problem of the noise characterization in the quantum sensitivity range is considered and a general noise parameter Theta(N) is introduced. This parameter is shown to be an adequate figure of merit for most receivers of interest while some devices can require a more complex characterization. Analytical expressions and/or numerically calculated plots for Theta(N) are presented for the most promising detection modes including the parametric amplification, heterodyne mixing, and quadratic videodetection, using both the quasiparticle-current and the Cooper-pair-current nonlinearities. Ultimate minimum values of Theta(N) for each detection mode are compared and found to be in agreement with limitations imposed by the quantum-mechanical uncertainty principle.

Manifestations of classical physics in the quantum evolution of correlated spin states in pulsed NMR experiments.

PubMed

Ligare, Martin

2016-05-01

Multiple-pulse NMR experiments are a powerful tool for the investigation of molecules with coupled nuclear spins. The product operator formalism provides a way to understand the quantum evolution of an ensemble of weakly coupled spins in such experiments using some of the more intuitive concepts of classical physics and semi-classical vector representations. In this paper I present a new way in which to interpret the quantum evolution of an ensemble of spins. I recast the quantum problem in terms of mixtures of pure states of two spins whose expectation values evolve identically to those of classical moments. Pictorial representations of these classically evolving states provide a way to calculate the time evolution of ensembles of weakly coupled spins without the full machinery of quantum mechanics, offering insight to anyone who understands precession of magnetic moments in magnetic fields.

HYDROGEN BONDING IN THE METHANOL DIMER

USDA-ARS?s Scientific Manuscript database

In this work, two methanol molecules are placed in different arrangements to study hydrogen bonding in carbohydrate materials such as cellulose. Energy was calculated as a function of both hydrogen bond length and angle over wide ranges, using quantum mechanics (QM). The QM wavefunctions are analyze...

Computer Series, 86. Bits and Pieces, 35.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1987-01-01

Describes eight applications of the use of computers in teaching chemistry. Includes discussions of audio frequency measurements of heat capacity ratios, quantum mechanics, ab initio calculations, problem solving using spreadsheets, simplex optimization, faradaic impedance diagrams, and the recording and tabulation of student laboratory data. (TW)

Atomic Calculations with a One-Parameter, Single Integral Method.

ERIC Educational Resources Information Center

Baretty, Reinaldo; Garcia, Carmelo

1989-01-01

Presents an energy function E(p) containing a single integral and one variational parameter, alpha. Represents all two-electron integrals within the local density approximation as a single integral. Identifies this as a simple treatment for use in an introductory quantum mechanics course. (MVL)

π -Stacking interactions in YFP, quantum mechanics and force field evaluations in the S0 and S1 states

NASA Astrophysics Data System (ADS)

Merabti, Karim Elhadj; Azizi, Sihem; Ridard, Jacqueline; Lévy, Bernard; Demachy, Isabelle

2017-08-01

We study the π -stacking interaction between the chromophore and Tyr203 in the Yellow Fluorescent Protein (YFP) in order to (i) evaluate the contribution of the internal interaction energy of the isolated Chromophore-Tyrosine complex (Eint) to the 26 nm red shift observed from GFP to YFP, (ii) compare the effects of Eint and of the proteic environment. To that end, we perform quantum mechanical and force field (ff) calculations of the isolated complex in S0 and S1 states on a large sample of geometries, together with molecular dynamics simulations and potential of mean force analysis. The calculated absorption wavelengths are found red shifted with respect to the isolated chromophore by 12-19 nm, that represents a large part of the GFP-YFP shift. We find that the effect of the protein is determinant on the dynamics of the complex while the error that results from using a classicalff is of limited effect.

Communication: Practical and rigorous reduction of the many-electron quantum mechanical Coulomb problem to O(N{sup 2/3}) storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pederson, Mark R., E-mail: mark.pederson@science.doe.gov

2015-04-14

It is tacitly accepted that, for practical basis sets consisting of N functions, solution of the two-electron Coulomb problem in quantum mechanics requires storage of O(N{sup 4}) integrals in the small N limit. For localized functions, in the large N limit, or for planewaves, due to closure, the storage can be reduced to O(N{sup 2}) integrals. Here, it is shown that the storage can be further reduced to O(N{sup 2/3}) for separable basis functions. A practical algorithm, that uses standard one-dimensional Gaussian-quadrature sums, is demonstrated. The resulting algorithm allows for the simultaneous storage, or fast reconstruction, of any two-electron Coulombmore » integral required for a many-electron calculation on processors with limited memory and disk space. For example, for calculations involving a basis of 9171 planewaves, the memory required to effectively store all Coulomb integrals decreases from 2.8 Gbytes to less than 2.4 Mbytes.« less

Quantum Mechanical Calculations of Free Energy and Open-Circuit Voltage in Lattice Modeled Organic Photovoltaic Devices

NASA Astrophysics Data System (ADS)

Lankevich, Vladimir; Bittner, Eric

In organic photovoltaic devices (OPVs), initially bound electron and hole can take many different paths to dissociate and become free charge carriers. This leads to the increase in their density of states and therefore increase in the entropy of the system. Accurate description of the energy barriers that charges have to overcome, therefore requires calculation of the free energy. Free energy of an OPV is directly related to its open-circuit voltage and depends only on few important parameters such as average life-time of a charge-transfer state, average energy of the charge-transfer state and energetic disorder in the system. We extend these ideas to the quantum mechanical simulations of the dissociation in the lattice modeled bulk-heterojunction system. We observe average excitonic and free energies that agree with theoretical predictions and the number of experimental results from previous studies. We study effects of the energy disorder and importance of the dimensionality and morphology in materials such as polymer-fullerene blends.

Molecular origin of differences in hole and electron mobility in amorphous Alq3--a multiscale simulation study.

PubMed

Fuchs, Andreas; Steinbrecher, Thomas; Mommer, Mario S; Nagata, Yuki; Elstner, Marcus; Lennartz, Christian

2012-03-28

In order to determine the molecular origin of the difference in electron and hole mobilities of amorphous thin films of Alq(3) (meridional Alq(3) (tris(8-hydroxyquinoline) aluminium)) we performed multiscale simulations covering quantum mechanics, molecular mechanics and lattice models. The study includes realistic disordered morphologies, polarized site energies to describe diagonal disorder, quantum chemically calculated transfer integrals for the off-diagonal disorder, inner sphere reorganization energies and an approximative scheme for outer sphere reorganization energies. Intermolecular transfer rates were calculated via Marcus-theory and mobilities were simulated via kinetic Monte Carlo simulations and by a Master Equation approach. The difference in electron and hole mobility originates from the different localization of charge density in the radical anion (more delocalized) compared to the radical cation (more confined). This results in higher diagonal disorder for holes and less favourable overlap properties for the hole transfer integrals leading to an overall higher electron mobility.

Schwarzschild radius from Monte Carlo calculation of the Wilson loop in supersymmetric matrix quantum mechanics.

PubMed

Hanada, Masanori; Miwa, Akitsugu; Nishimura, Jun; Takeuchi, Shingo

2009-05-08

In the string-gauge duality it is important to understand how the space-time geometry is encoded in gauge theory observables. We address this issue in the case of the D0-brane system at finite temperature T. Based on the duality, the temporal Wilson loop W in gauge theory is expected to contain the information of the Schwarzschild radius RSch of the dual black hole geometry as log(W)=RSch/(2pialpha'T). This translates to the power-law behavior log(W)=1.89(T/lambda 1/3)-3/5, where lambda is the 't Hooft coupling constant. We calculate the Wilson loop on the gauge theory side in the strongly coupled regime by performing Monte Carlo simulations of supersymmetric matrix quantum mechanics with 16 supercharges. The results reproduce the expected power-law behavior up to a constant shift, which is explainable as alpha' corrections on the gravity side. Our conclusion also demonstrates manifestly the fuzzball picture of black holes.

Communication: practical and rigorous reduction of the many-electron quantum mechanical Coulomb problem to O(N(2/3)) storage.

PubMed

Pederson, Mark R

2015-04-14

It is tacitly accepted that, for practical basis sets consisting of N functions, solution of the two-electron Coulomb problem in quantum mechanics requires storage of O(N(4)) integrals in the small N limit. For localized functions, in the large N limit, or for planewaves, due to closure, the storage can be reduced to O(N(2)) integrals. Here, it is shown that the storage can be further reduced to O(N(2/3)) for separable basis functions. A practical algorithm, that uses standard one-dimensional Gaussian-quadrature sums, is demonstrated. The resulting algorithm allows for the simultaneous storage, or fast reconstruction, of any two-electron Coulomb integral required for a many-electron calculation on processors with limited memory and disk space. For example, for calculations involving a basis of 9171 planewaves, the memory required to effectively store all Coulomb integrals decreases from 2.8 Gbytes to less than 2.4 Mbytes.

Pressure-induced Structural Transformations in LanthanideTitanates: La2TiO5 and Nd2TiO5

DOE Office of Scientific and Technical Information (OSTI.GOV)

F Zhang; J Wang; M Lang

The structure of orthorhombic rare earth titanates of La{sub 2}TiO{sub 5} and Nd{sub 2}TiO{sub 5}, where Ti cations are in five-fold coordination with oxygen, has been studied at high pressures by X-ray diffraction (XRD), Raman scattering measurements, and quantum mechanical calculations. Both XRD and Raman results indicated two pressure-induced phase transitions during the process. An orthorhombic super cell (a x b x 2c) formed at a pressure between 6 and 10 GPa, and then transformed to a hexagonal high-pressure phase accompanied by partial decomposition. The hexagonal high-pressure phase is quenchable. Detailed structural analysis indicated that the five-coordinated TiO{sub 5} polyhedramore » remain during the formation of super cell, but the orthorhombic-to-hexagonal phase transition at high pressures is a reconstructive process, and the five-fold Ti-O coordination increased to more than 6. This phase transition sequence was verified by quantum mechanical calculations.« less

First-Principles Studies of Structure-Property Relationships: Enabling Design of Functional Materials

NASA Astrophysics Data System (ADS)

Zhou, Qunfei

First-principles calculations based on quantum mechanics have been proved to be powerful for accurately regenerating experimental results, uncovering underlying myths of experimental phenomena, and accelerating the design of innovative materials. This work has been motivated by the demand to design next-generation thermionic emitting cathodes and techniques to allow for synthesis of photo-responsive polymers on complex surfaces with controlled thickness and patterns. For Os-coated tungsten thermionic dispenser cathodes, we used first-principles methods to explore the bulk and surface properties of W-Os alloys in order to explain the previously observed experimental phenomena that thermionic emission varies significantly with W-Os alloy composition. Meanwhile, we have developed a new quantum mechanical approach to quantitatively predict the thermionic emission current density from materials perspective without any semi-empirical approximations or complicated analytical models, which leads to better understanding of thermionic emission mechanism. The methods from this work could be used to accelerate the design of next-generation thermionic cathodes. For photoresponsive materials, we designed a novel type of azobenzene-containing monomer for light-mediated ring-opening metathesis polymerization (ROMP) toward the fabrication of patterned, photo-responsive polymers by controlling ring strain energy (RSE) of the monomer that drives ROMP. This allows for unprecedented remote, noninvasive, instantaneous spatial and temporal control of photo-responsive polymer deposition on complex surfaces.This work on the above two different materials systems showed the power of quantum mechanical calculations on predicting, understanding and discovering the structures and properties of both known and unknown materials in a fast, efficient and reliable way.

Development and Use of Numerical and Factual Data Bases

DTIC Science & Technology

1983-10-01

the quantitative description of what has been accomplished by their scientific and technical endeavors. 1-3 overhead charge to the national treasury... Molecular properties calculated with the aid of quantum mechanics or the prediction of solar eclipses using celestial mechanics are examples of theoretical...system under study. Examples include phase diagrams, molecular models, geological maps, metabolic pathways. Symbolic data (F3) are data presented in

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Quantum mechanics in complex systems

NASA Astrophysics Data System (ADS)

Hoehn, Ross Douglas

This document should be considered in its separation; there are three distinct topics contained within and three distinct chapters within the body of works. In a similar fashion, this abstract should be considered in three parts. Firstly, we explored the existence of multiply-charged atomic ions by having developed a new set of dimensional scaling equations as well as a series of relativistic augmentations to the standard dimensional scaling procedure and to the self-consistent field calculations. Secondly, we propose a novel method of predicting drug efficacy in hopes to facilitate the discovery of new small molecule therapeutics by modeling the agonist-protein system as being similar to the process of Inelastic Electron Tunneling Spectroscopy. Finally, we facilitate the instruction in basic quantum mechanical topics through the use of quantum games; this method of approach allows for the generation of exercises with the intent of conveying the fundamental concepts within a first year quantum mechanics classroom. Furthermore, no to be mentioned within the body of the text, yet presented in appendix form, certain works modeling the proliferation of cells types within the confines of man-made lattices for the purpose of facilitating artificial vascular transplants. In Chapter 2, we present a theoretical framework which describes multiply-charged atomic ions, their stability within super-intense laser fields, also lay corrections to the systems due to relativistic effects. Dimensional scaling calculations with relativistic corrections for systems: H, H-, H 2-, He, He-, He2-, He3- within super-intense laser fields were completed. Also completed were three-dimensional self consistent field calculations to verify the dimensionally scaled quantities. With the aforementioned methods the system's ability to stably bind 'additional' electrons through the development of multiple isolated regions of high potential energy leading to nodes of high electron density is shown. These nodes are spaced far enough from each other to minimized the electronic repulsion of the electrons, while still providing adequate enough attraction so as to bind the excess elections into orbitals. We have found that even with relativistic considerations these species are stably bound within the field. It was also found that performing the dimensional scaling calculations for systems within the confines of laser fields to be a much simpler and more cost-effective method than the supporting D=3 SCF method. The dimensional scaling method is general and can be extended to include relativistic corrections to describe the stability of simple molecular systems in super-intense laser fields. Chapter 3, we delineate the model, and aspects therein, of inelastic electron tunneling and map this model to the protein environment. G protein-coupled receptors (GPCRs) constitute a large family of receptors that sense molecules outside of a cell and activate signal transduction pathways inside the cell. Modeling how an agonist activates such a receptor is important for understanding a wide variety of physiological processes and it is of tremendous value for pharmacology and drug design. Inelastic electron tunneling spectroscopy (IETS) has been proposed as the mechanism by which olfactory GPCRs are activated by an encapsulated agonist. In this note we apply this notion to GPCRs within the mammalian nervous system using ab initio quantum chemical modeling. We found that non-endogenous agonists of the serotonin receptor share a singular IET spectral aspect both amongst each other and with the serotonin molecule: a peak that scales in intensity with the known agonist activities. We propose an experiential validation of this model by utilizing lysergic acid dimethylamide (DAM-57), an ergot derivative, and its isotopologues in which hydrogen atoms are replaced by deuterium. If validated our theory may provide new avenues for guided drug design and better in silico prediction of efficacies. Our final chapter, explores methods which may be explored to assist in the early instruction in quantum mechanics. The learning of quantum mechanics is contingent upon an understanding of the physical significance of the mathematics that one must perform. Concepts such as normalization, superposition, interference, probability amplitude and entanglement can prove challenging for the beginning student. This paper outlines several class exercises that use a non-classical version of tic-tac-toe to instruct several topics in an undergraduate quantum mechanics course. Quantum tic-tac-toe (QTTT) is a quantum analogue of classical tic-tac-toe (CTTT) benefiting from the use of superposition in movement, qualitative (and later quantitative) displays of entanglement and state collapse due to observation. QTTT can be used for the benefit of the students understanding in several other topics with the aid of proper discussion.

An unscaled quantum mechanical harmonic force field for p-benzoquinone

NASA Astrophysics Data System (ADS)

Nonella, Marco; Tavan, Paul

1995-10-01

Structure and harmonic vibrational frequencies of p-benzoquinone have been calculated using quantum chemical ab initio and density functional methods. Our calculations show that a satisfactory description of fundamentals and normal mode compositions is achieved upon consideration of correlation effects by means of Møller-Plesset perturbation expansion (MP2) or by density functional theory (DFT). Furthermore, for correct prediction of CO bondlength and force constant, basis sets augmented by polarization functions are required. Applying such basis sets, MP2 and DFT calculations both give results which are generally in reasonable agreement with experimental data. The quantitatively better agreement, however, is achieved with the computationally less demanding DFT method. This method particularly allows very precise prediction of the experimentally important absorptions in the frequency region between 1500 and 1800 cm -1 and of the isotopic shifts of these vibrations due to 13C or 18O substitution.

Stabilization of the Simplest Criegee Intermediate from the Reaction between Ozone and Ethylene: A High-Level Quantum Chemical and Kinetic Analysis of Ozonolysis.

PubMed

Nguyen, Thanh Lam; Lee, Hyunwoo; Matthews, Devin A; McCarthy, Michael C; Stanton, John F

2015-06-04

The fraction of the collisionally stabilized Criegee species CH2OO produced from the ozonolysis of ethylene is calculated using a two-dimensional (E, J)-grained master equation technique and semiclassical transition-state theory based on the potential energy surface obtained from high-accuracy quantum chemical calculations. Our calculated yield of 42 ± 6% for the stabilized CH2OO agrees well, within experimental error, with available (indirect) experimental results. Inclusion of angular momentum in the master equation is found to play an essential role in bringing the theoretical results into agreement with the experiment. Additionally, yields of HO and HO2 radical products are predicted to be 13 ± 6% and 17 ± 6%, respectively. In the kinetic simulation, the HO radical product is produced mostly from the stepwise decomposition mechanism of primary ozonide rather than from dissociation of hot CH2OO.

Entangled quantum electronic wavefunctions of the Mn₄CaO₅ cluster in photosystem II.

PubMed

Kurashige, Yuki; Chan, Garnet Kin-Lic; Yanai, Takeshi

2013-08-01

It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 10(18) quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle.

Unveiling the composite structures of emissive consolidated p-i-n junction nanocells for white light emission.

PubMed

Lee, Kyu Seung; Shim, Jaeho; Lee, Hyunbok; Yim, Sang-Youp; Angadi, Basavaraj; Lim, Byungkwon; Son, Dong Ick

2018-06-08

Hybrid organic-Red-Green-Blue (RGB) color quantum dots were incorporated into consolidated p(polymer)-i(RGB quantum dots)-n(small molecules) junction structures to fabricate a single active layer for a light emitting diode device for white electroluminescence. The semiconductor RGB quantum dots, as an intrinsic material, were electrostatically bonded between functional groups of the p-type polymer organic material core surface and the n-type small molecular organic material shell surface. The ZnCdSe/ZnS and CdSe/ZnS quantum dots distributed uniformly and isotropically surrounding the polymer core which in turn was surrounded by small molecular organic materials. In the present study, we have identified the mechanisms of chemical synthesis and interactions of the p-i-n junction nanocell structure through modeling studies by DFT calculations. We have also investigated optical, structural and electrical properties along with the carrier transport mechanism of the light emitting diodes which have a single active layer of consolidated p-i-n junction nanocells for white electroluminescence.

Experimental and theoretical investigation of the elastic moduli of silicate glasses and crystals

NASA Astrophysics Data System (ADS)

Philipps, Katharina; Stoffel, Ralf Peter; Dronskowski, Richard; Conradt, Reinhard

2017-02-01

A combined quantum-mechanical and thermodynamic approach to the mechanical properties of multicomponent silicate glasses is presented. Quantum chemical calculations based on density-functional theory (DFT) on various silicate systems were performed to explore the crystalline polymorphs existing for a given chemical composition. These calculations reproduced the properties of known polymorphs even in systems with extensive polymorphism, like MgSiO3. Properties resting on the atomic and electronic structure, i.e., molar volumes (densities) and bulk moduli were predicted correctly. The theoretical data (molar equilibrium volumes, bulk moduli) were then used to complement the available experimental data. In a phenomenological evaluation, experimental data of bulk moduli, a macroscopic property resting on phononic structure, were found to linearly scale with the ratios of atomic space demand to actual molar volume in a universal way. Silicates ranging from high-pressure polymorphs to glasses were represented by a single master line. This suggests that above the Debye limit (in practice: above room temperature), the elastic waves probe the short range order coordination polyhedra and their next-neighbor linkage only, while the presence or absence of an extended translational symmetry is irrelevant. As a result, glasses can be treated - with respect to the properties investigated - as commensurable members of polymorphic series. Binary glasses fit the very same line as their one-component end-members, again both in the crystalline and glassy state. Finally, it is shown that the macroscopic properties of multicomponent glasses also are linear superpositions of the properties of their constitutional phases (as determined from phase diagrams or by thermochemical calculations) taken in their respective glassy states. This is verified experimentally for heat capacities and Young’s moduli of industrial glass compositions. It can be concluded, that the combined quantum mechanical and thermochemical approach is a truly quantitative approach for the design of glasses with desired mechanical properties, e.g., for the development of high-modulus glasses.

Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study

NASA Astrophysics Data System (ADS)

Lee, Vannajan Sanghiran; Kodchakorn, Kanchanok; Jitonnom, Jitrayut; Nimmanpipug, Piyarat; Kongtawelert, Prachya; Premanode, Bhusana

2010-10-01

The reaction mechanism of creatinine-creatininase binding to form creatine as a final product has been investigated by using a combined ab initio quantum mechanical/molecular mechanical approach and classical molecular dynamics (MD) simulations. In MD simulations, an X-ray crystal structure of the creatininase/creatinine was modified for creatininase/creatinine complexes and the MD simulations were run for free creatininase and creatinine in water. MD results reveal that two X-ray water molecules can be retained in the active site as catalytic water. The binding free energy from Molecular Mechanics Poisson-Boltzmann Surface Area calculation predicted the strong binding of creatinine with Zn2+, Asp45 and Glu183. Two step mechanisms via Mn2+/Zn2+ (as in X-ray structure) and Zn2+/Zn2+ were proposed for water adding step and ring opening step with two catalytic waters. The pathway using synchronous transit methods with local density approximations with PWC functional for the fragment in the active region were obtained. Preferable pathway Zn2+/Zn2+ was observed due to lower activation energy in water adding step. The calculated energy in the second step for both systems were comparable with the barrier of 26.03 and 24.44 kcal/mol for Mn2+/Zn2+ and Zn2+/Zn2+, respectively.

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

Enzymatic studies using quantum mechanical and molecular mechanical techniques

NASA Astrophysics Data System (ADS)

Faulder, Paul F.

Enzymes have evolved to increase the rate of biological reactions using fundamental physical processes. Until recently, the nature of catalysis has been based upon a classical model but it has since been considered that certain aspects of catalysis, particularly those concerning the transfer of a hydrogen species, may be accounted for using the theory of quantum mechanics. This thesis reports the use of reaction paths obtained using QMMM (combined quantum mechanics-molecular mechanics), combined with canonical variational transition state theory and multidimensional tunnelling corrections, to study two dehydrogenase enzymes, Liver Alcohol Dehydrogenase (LADH) and Methylamine Dehydrogenase (MADH). These methods are used to investigate the nature of these models in explaining reported experimental data indicative of quantum mechanical tunnelling within these enzymes. The results obtained are in good agreement with experimental data indicating the presence of tunnelling in LADH and, to a greater degree, in MADH, reflected in the magnitude of the calculated kinetic isotope effects (KIEs). For LADH, a primary tritium KIE of 5.6 is reported, calculated using transition state theory (TST) with a Wigner tunnelling correction, and compares favourably with an experimental value of 7.1. For MADH, a KIE of 11.1 was determined using canonical variational theory (CVT) with a small curvature tunnelling (SCT) correction, and compared favourably with an experimental value of 16.8. In addition, a relationship is observed between the contribution due to tunnelling in each system and the geometric positioning of the donating and accepting atoms of the transferring species, and is in qualitative agreement with current opinion concerning tunnelling and the dynamic nature of catalysis. Potential energy barriers have been obtained for both systems using QMMM. For LADH, barriers of 8.2 kcal mol-1 and 22.0 kcal mol-1, and reaction energies of -25.7 kcal mol-1 and +3.4 kcal mol-1, are reported for PM3 semiempirical and HF/3-21G respectively compared with an experimental barrier of 15.6 kcal mol-1 and reaction energy of +1.0 kcal mol-1. In MADH, a potential energy barrier of 9.1 kcal mol-1 is reported for PM3, compared with 10.7 kcal mol-1 experimentally. A reaction energy of -3.5 kcal mol-1 is also reported although no experimental data is available for comparison. All ah initio calculations produced significantly higher barriers and endothermic reaction energies. Chapter 1 presents a review of protein structure and classical enzyme catalysis, providing the foundations for a discussion of recent work concerning the application of quantum tunnelling in rationalising catalysis in certain enzymatic systems. Chapter 2 utilises the background information provided in Chapter 1 in a discussion specifically applied to previous experimental data concerning the structure, function and catalytic behaviour reported for the enzymes LADH and MADH. Chapter 3 presents a background to the methodology behind the theoretical methods used in the investigation of LADH and MADH reported in this thesis, in addition to reporting the development of extra code which has allowed the integration of our QMMM software with the rate determining program, POLYRATE, allowing the calculation of KIEs for these enzymes. Chapter 4 presents the preparation of the enzyme model of LADH with two separate substrates and the results obtained from subsequent QMMM calculations carried out on these models. These results are presented alongside results obtained by other workers, for comparative analysis. Chapter 5 details the preparation of a model of MADH with the substrate methylamine, and the QMMM investigation of the mode of catalysis for this enzyme using a variety of separate QMMM models. The calculation of KIEs on this enzyme, using the modified POLYRATE, are then presented in addition to KIEs determined for LADH based on results obtained from Chapter 4, and are discussed. The results of QMMM calculations carried out on MADH from a separate species are then presented in the context of validating the first set of results. Finally, QMMM calculations are presented for MADH bound to the substrate ethanolamine, attempting to elucidate the catalytically similar mechanism to methylamine.

Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

NASA Astrophysics Data System (ADS)

Legler, C. R.; Brown, N. R.; Dunbar, R. A.; Harness, M. D.; Nguyen, K.; Oyewole, O.; Collier, W. B.

2015-06-01

The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

Quantum mechanical force fields for condensed phase molecular simulations

NASA Astrophysics Data System (ADS)

Giese, Timothy J.; York, Darrin M.

2017-09-01

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

Quantum Electron Tunneling in Respiratory Complex I1

PubMed Central

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.

2014-01-01

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. One-electron tunneling approximation is found to hold in electron tunneling between the anti-ferromagnetic binuclear and tetranuclear Fe/S clusters with moderate induced polarization of the core electrons. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A distinct signature of the wave properties of electrons is observed as quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included are in good agreement with a reported phenomenological relation. PMID:21495666

State-selected chemical reaction dynamics at the S matrix level - Final-state specificities of near-threshold processes at low and high energies

NASA Technical Reports Server (NTRS)

Chatfield, David C.; Truhlar, Donald G.; Schwenke, David W.

1992-01-01

State-to-state reaction probabilities are found to be highly final-state specific at state-selected threshold energies for the reactions O + H2 yield OH + H and H + H2 yield H2 + H. The study includes initial rotational states with quantum numbers 0-15, and the specificity is especially dramatic for the more highly rotationally excited reactants. The analysis is based on accurate quantum mechanical reactive scattering calculations. Final-state specificity is shown in general to increase with the rotational quantum number of the reactant diatom, and the trends are confirmed for both zero and nonzero values of the total angular momentum.

Carrier relaxation mechanisms in self-assembled (In,Ga)As/GaAs quantum dots: Efficient P→S Auger relaxation of electrons

NASA Astrophysics Data System (ADS)

Narvaez, Gustavo A.; Bester, Gabriel; Zunger, Alex

2006-08-01

We calculate the P -shell-to- S -shell decay lifetime τ(P→S) of electrons in lens-shaped self-assembled (In,Ga)As/GaAs dots due to Auger electron-hole scattering within an atomistic pseudopotential-based approach. We find that this relaxation mechanism leads to fast decay of τ(P→S)˜1-7ps for dots of different sizes. Our calculated Auger-type P -shell-to- S -shell decay lifetimes τ(P→S) compare well to data in (In,Ga)As/GaAs dots, showing that as long as both electrons and holes are present there is no need for an alternative polaron mechanism.

Quantum heat engine with coupled superconducting resonators

NASA Astrophysics Data System (ADS)

Hardal, Ali Ü. C.; Aslan, Nur; Wilson, C. M.; Müstecaplıoǧlu, Özgür E.

2017-12-01

We propose a quantum heat engine composed of two superconducting transmission line resonators interacting with each other via an optomechanical-like coupling. One resonator is periodically excited by a thermal pump. The incoherently driven resonator induces coherent oscillations in the other one due to the coupling. A limit cycle, indicating finite power output, emerges in the thermodynamical phase space. The system implements an all-electrical analog of a photonic piston. Instead of mechanical motion, the power output is obtained as a coherent electrical charging in our case. We explore the differences between the quantum and classical descriptions of our system by solving the quantum master equation and classical Langevin equations. Specifically, we calculate the mean number of excitations, second-order coherence, as well as the entropy, temperature, power, and mean energy to reveal the signatures of quantum behavior in the statistical and thermodynamic properties of the system. We find evidence of a quantum enhancement in the power output of the engine at low temperatures.

Quantum heat engine with coupled superconducting resonators.

PubMed

Hardal, Ali Ü C; Aslan, Nur; Wilson, C M; Müstecaplıoğlu, Özgür E

2017-12-01

We propose a quantum heat engine composed of two superconducting transmission line resonators interacting with each other via an optomechanical-like coupling. One resonator is periodically excited by a thermal pump. The incoherently driven resonator induces coherent oscillations in the other one due to the coupling. A limit cycle, indicating finite power output, emerges in the thermodynamical phase space. The system implements an all-electrical analog of a photonic piston. Instead of mechanical motion, the power output is obtained as a coherent electrical charging in our case. We explore the differences between the quantum and classical descriptions of our system by solving the quantum master equation and classical Langevin equations. Specifically, we calculate the mean number of excitations, second-order coherence, as well as the entropy, temperature, power, and mean energy to reveal the signatures of quantum behavior in the statistical and thermodynamic properties of the system. We find evidence of a quantum enhancement in the power output of the engine at low temperatures.

Quantum gravity in the Southern Cone Conference. Proceedings. Conference, Bariloche (Argentina), 7 - 10 Jan 1998.

NASA Astrophysics Data System (ADS)

1999-04-01

The following topics are discussed: Black hole formation by canonical dynamics of gravitating shells; canonical quantum gravity; Vassiliev invariants; midisuperspace models; quantum spacetime; large-N limit of superconformal field theories and supergravity; world-volume fields and background coupling of branes; gauge enhancement and chirality changes in nonperturbative orbifold models; chiral p-forms; formally renormalizable gravitationally self-interacting string models; gauge supergravities for all odd dimensions; black hole radiation and S-matrix; primordial black holes; fluctuations in a thermal field and dissipation of a black hole spacetime in far-field limit; adiabatic interpretation of particle creation in a de Sitter universe; nonequilibrium dynamics of quantum fields in inflationary cosmology; magnetic fields in the early Universe; classical regime of a quantum universe obtained through a functional method; decoherence and correlations in semiclassical cosmology; fluid of primordial fluctuations; causal statistical mechanics calculation of initial cosmic entropy and quantum gravity prospects and black hole-D-brane correspondence.

Vibrational and UV spectroscopic studies of 2-coumaranone by experimental and density functional theory calculations

NASA Astrophysics Data System (ADS)

Priya, Y. Sushma; Rao, K. Ramachandra; Chalapathi, P. V.; Satyavani, M.; Veeraiah, A.

2017-09-01

The vibrational and electronic properties of 2-coumaranone have been reported in the ground state using experimental techniques (FT-IR, FT-Raman, UV spectra and fluorescence microscopic imaging) and density functional theory (DFT) employing B3LYP correlation with the 6-31G(d, p) basis set. The theoretically reported optimized parameters, vibrational frequencies etc., were compared with the experimental values, which yielded good concurrence between the experimental and calculated values. The assignments of the vibrational spectra were done with the help of normal co-ordinate analysis (NCA) following the Scaled Quantum Mechanical Force Field(SQMFF) methodology. The whole assignments of fundamental modes were based on the potential energy distribution (PED) matrix. The electric dipole moment and the first order hyperpolarizability of the 2-coumaranone have been computed using quantum mechanical calculations. NBO and HOMO, LUMO analyses have been carried out. UV spectrum of 2-coumaranone was recorded in the region 100-300 nm and compared with the theoretical UV spectrum using TD-DFT and SAC-CI methods by which a good agreement is observed. Fluorescence microscopic imaging study reflects that the compound fluoresces in the green-yellow region.

Polarizabilities and van der Waals C{sub 6} coefficients of fullerenes from an atomistic electrodynamics model: Anomalous scaling with number of carbon atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saidi, Wissam A., E-mail: alsaidi@pitt.edu; Norman, Patrick

2016-07-14

The van der Waals C{sub 6} coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C{sub 6} ∝ N{sup 2.2} as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N{sup 2.75} as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes bymore » fitting against accurate ab initio calculations. This model shows that C{sub 6} ∝ N{sup 2.8}, which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole–dipole term scales almost linearly with the number of carbon atoms.« less

Effects of bias and temperature on the intersubband absorption in very long wavelength GaAs/AlGaAs quantum well infrared photodetectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, X. H.; Zhou, X. H., E-mail: xhzhou@mail.sitp.ac.cn; Li, N.

2014-03-28

The temperature- and bias-dependent photocurrent spectra of very long wavelength GaAs/AlGaAs quantum well infrared photodetectors (QWIPs) are studied using spectroscopic measurements and corresponding theoretical calculations. It is found that the peak response wavelength will shift as the bias and temperature change. Aided by band structure calculations, we propose a model of the double excited states and explain the experimental observations very well. In addition, the working mechanisms of the quasi-bound state confined in the quantum well, including the processes of tunneling and thermionic emission, are also investigated in detail. We confirm that the first excited state, which belongs to themore » quasi-bound state, can be converted into a quasi-continuum state induced by bias and temperature. These obtained results provide a full understanding of the bound-to-quasi-bound state and the bound-to-quasi-continuum state transition, and thus allow for a better optimization of QWIPs performance.« less

More on homological supersymmetric quantum mechanics

NASA Astrophysics Data System (ADS)

Behtash, Alireza

2018-03-01

In this work, we first solve complex Morse flow equations for the simplest case of a bosonic harmonic oscillator to discuss localization in the context of Picard-Lefschetz theory. We briefly touch on the exact non-BPS solutions of the bosonized supersymmetric quantum mechanics on algebraic geometric grounds and report that their complex phases can be accessed through the cohomology of WKB 1-form of the underlying singular spectral curve subject to necessary cohomological corrections for nonzero genus. Motivated by Picard-Lefschetz theory, we write down a general formula for the index of N =4 quantum mechanics with background R -symmetry gauge fields. We conjecture that certain symmetries of the refined Witten index and singularities of the moduli space may be used to determine the correct intersection coefficients. A few examples, where this conjecture holds, are shown in both linear and closed quivers with rank-one quiver gauge groups. The R -anomaly removal along the "Morsified" relative homology cycles also called "Lefschetz thimbles" is shown to lead to the appearance of Stokes lines. We show that the Fayet-Iliopoulos parameters appear in the intersection coefficients for the relative homology of the quiver quantum mechanics resulting from dimensional reduction of 2 d N =(2 ,2 ) gauge theory on a circle and explicitly calculate integrals along the Lefschetz thimbles in N =4 C Pk -1 model. The Stokes jumping of coefficients and its relation to wall crossing phenomena is briefly discussed. We also find that the notion of "on-the-wall" index is related to the invariant Lefschetz thimbles under Stokes phenomena. An implication of the Lefschetz thimbles in constructing knots from quiver quantum mechanics is indicated.

Zwitterionization of glycine in water environment: Stabilization mechanism and NMR spectral signatures

NASA Astrophysics Data System (ADS)

Valverde, Danillo; da Costa Ludwig, Zélia Maria; da Costa, Célia Regina; Ludwig, Valdemir; Georg, Herbert C.

2018-01-01

At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach. A series of Monte Carlo Metropolis simulations of the glycine molecule embedded in liquid water, followed by only a quantum mechanical calculation in each of them were carried out. Both the local and global liquid environments were emphasized to obtain nuclear magnetic resonance (NMR) parameters for the glycine molecule in liquid water. The results of the equilibrium structure in solution and the systematic study of the hydrogen bonds were used to discard the direct proton transfer from the carboxyl group to the ammonium group of the glycine molecule in water solution. The calculations of the Density Functional Theory (DFT) were performed to study the polarization of the solvent in the parameters of nuclear magnetic resonance of the glycine molecule in liquid water. DFT calculations predicted isotropic chemical changes on the H, C, N, and O atoms of glycine in liquid water solution which agree with the available experimental data.

Wronskian Method for Bound States

ERIC Educational Resources Information Center

Fernandez, Francisco M.

2011-01-01

We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider…

Predicted phototoxicities of carbon nano-material by quantum mechanical calculations.

PubMed

Betowski, Don

2017-08-01

The purpose of this research was to develop a predictive model for the phototoxicity potential of carbon nanomaterials (fullerenols and single-walled carbon nanotubes). This model is based on the quantum mechanical (ab initio) calculations on these carbon-based materials and comparison of the triplet excited states of these materials to published work relating phototoxicity of polynuclear aromatic hydrocarbons (PAH) to their predictive triplet excited state energy. A successful outcome will add another tool to the arsenal of predictive methods for the U.S. EPA program offices as they assess the toxicity of compounds in use or coming into commerce. The basis of this research was obtaining the best quantum mechanical structure of the carbon nanomaterial and was fundamental in determining the triplet excited state energy. The triplet excited state, in turn, is associated with the phototoxicity of the material. This project relies heavily on the interaction of the predictive results (physical chemistry) and the experimental results obtained by biologists and toxicologists. The results of the experiments (toxicity testing) will help refine the predictive model, while the predictions will alert the scientists to red flag compounds. It is hoped that a guidance document for the U.S. EPA will be forthcoming to help determine the toxicity of compounds. This can be a screening tool that would rely on further testing for those compounds found by these predictions to be a phototoxic danger to health and the environment. Copyright © 2017. Published by Elsevier Inc.

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

PubMed

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

2011-03-15

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

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum–classical approximation. II. Proton transfer reaction in non-polar solvent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kojima, H.; Yamada, A.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp

2015-05-07

The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum–classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates ismore » reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute–solvent interactions.« less

Drama in Dynamics: Boom, Splash, and Speed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Netzloff, Heather Marie

2004-12-19

The full nature of chemistry and physics cannot be captured by static calculations alone. Dynamics calculations allow the simulation of time-dependent phenomena. This facilitates both comparisons with experimental data and the prediction and interpretation of details not easily obtainable from experiments. Simulations thus provide a direct link between theory and experiment, between microscopic details of a system and macroscopic observed properties. Many types of dynamics calculations exist. The most important distinction between the methods and the decision of which method to use can be described in terms of the size and type of molecule/reaction under consideration and the type andmore » level of accuracy required in the final properties of interest. These considerations must be balanced with available computational codes and resources as simulations to mimic ''real-life'' may require many time steps. As indicated in the title, the theme of this thesis is dynamics. The goal is to utilize the best type of dynamics for the system under study while trying to perform dynamics in the most accurate way possible. As a quantum chemist, this involves some level of first principles calculations by default. Very accurate calculations of small molecules and molecular systems are now possible with relatively high-level ab initio quantum chemistry. For example, a quantum chemical potential energy surface (PES) can be developed ''on-the-fly'' with dynamic reaction path (DRP) methods. In this way a classical trajectory is developed without prior knowledge of the PES. In order to treat solvation processes and the condensed phase, large numbers of molecules are required, especially in predicting bulk behavior. The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute and an ''effective fragment'' region that contains the remaining solvent molecules. But, despite the reduced cost relative to fully QM calculations, the EFP method, due to its complex, QM-based potential, does require more computation time than simple interaction potentials, especially when the method is used for large scale molecular dynamics simulations. Thus, the EFP method was parallelized to facilitate these calculations within the quantum chemistry program GAMESS. The EFP method provides relative energies and structures that are in excellent agreement with the analogous fully quantum results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. Molecular dynamics simulations can provide properties that are directly comparable with experimental results, for example radial distribution functions. The molecular PES is a fundamental starting point for chemical reaction dynamics. Many methods can be used to obtain a PES; for example, assuming a global functional form for the PES or, as mentioned above, performing ''on-the-fly'' dynamics with Al or semi-empirical calculations at every molecular configuration. But as the size of the system grows, using electronic structure theory to build a PES and, therefore, study reaction dynamics becomes virtually impossible. The program Grow builds a PES as an interpolation of Al data; the goal is to attempt to produce an accurate PES with the smallest number of Al calculations. The Grow-GAMESS interface was developed to obtain the Al data from GAMESS. Classical or quantum dynamics can be performed on the resulting surface. The interface includes the novel capability to build multi-reference PESs; these types of calculations are applicable to problems ranging from atmospheric chemistry to photochemical reaction mechanisms in organic and inorganic chemistry to fundamental biological phenomena such as photosynthesis.« less

The direct reaction field hamiltonian: Analysis of the dispersion term and application to the water dimer

NASA Astrophysics Data System (ADS)

Thole, B. T.; Van Duijnen, P. Th.

1982-10-01

The induction and dispersion terms obtained from quantum-mechanical calculations with a direct reaction field hamiltonian are compared to second order perturbation theory expressions. The dispersion term is shown to give an upper bound which is a generalization of Alexander's upper bound. The model is illustrated by a calculation on the interactions in the water dimer. The long range Coulomb, induction and dispersion interactions are reasonably reproduced.

Molecular structure, electronic properties, NLO, NBO analysis and spectroscopic characterization of Gabapentin with experimental (FT-IR and FT-Raman) techniques and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Sinha, Leena; Karabacak, Mehmet; Narayan, V.; Cinar, Mehmet; Prasad, Onkar

2013-05-01

Gabapentin (GP), structurally related to the neurotransmitter GABA (gamma-aminobutyric acid), mimics the activity of GABA and is also widely used in neurology for the treatment of peripheral neuropathic pain. It exists in zwitterionic form in solid state. The present communication deals with the quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of GP using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. In view of the fact that amino acids exist as zwitterions as well as in the neutral form depending on the environment (solvent, pH, etc.), molecular properties of both the zwitterionic and neutral form of GP have been analyzed. The fundamental vibrational wavenumbers as well as their intensities were calculated and compared with experimental FT-IR and FT-Raman spectra. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The electric dipole moment, polarizability and the first hyperpolarizability values of the GP have been calculated at the same level of theory and basis set. The nonlinear optical (NLO) behavior of zwitterionic and neutral form has been compared. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV-Vis) spectrum of the title molecule has also been calculated using TD-DFT method. The thermodynamic properties of both the zwitterionic and neutral form of GP at different temperatures have been calculated.

Comment on 'Realism and quantum flux tunneling'

NASA Technical Reports Server (NTRS)

Leggett, A. J.; Garg, Anupam

1987-01-01

A reply is presented to Ballentine's (1987) critique of the Legett and Garg (1985) experiment to discriminate between the experimental predictions of quantum mechanics (QM) and those of a class of macrorealistic theories. Legett and Garg uphold their earlier conclusions on the basis of the fact that the present critique refers to an experiment which was not in fact proposed. It is stressed that the original work involved an analysis according to macrorealism, while the calculations of Ballentine only demonstrate the internal consistency of the formalism of QM when applied to three consecutive actually performed experiments.

Effects of quantum interference between radiative and dielectronic recombination on photorecombination cross-section profiles for the He-like ions Ar{sup 16+} and Fe{sup 24+}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Behar, Ehud; Jacobs, Verne L.; Oreg, Joseph

Total cross sections for electron-ion photorecombination (PR) processes are calculated using a projection-operator and resolvent-operator approach. This approach provides a unified quantum-mechanical description of the combined electron-ion PR process, including radiative and dielectronic recombination as coherent, interfering components. An especially adapted version of the Hebrew-University Lawrence-Livermore Atomic Code HULLAC is developed and employed for the calculations. In particular, PR cross sections for He-like argon and iron ions are calculated for incident-electron energies in the vicinity of the 1s2l2l{sup '} and 1s2l3l{sup '} doubly-excited, autoionizing levels of the Li-like ions. Significant effects of quantum interference between radiative and dielectronic recombination, inmore » the form of asymmetric PR cross-section profiles, are predicted, especially for weak transitions. The general behavior of the interference effect, as a function of the ion charge q and as a function of the principal quantum number n{sup '} of the outer electron in the autoionizing state, is investigated using a hydrogenic-scaling analysis. It is found that the degree of asymmetry in the PR cross-section profile can be substantial for close-to-neutral ions and also for very highly-charged ions. In the intermediate-charge regime, on the other hand, the asymmetry is anticipated to be less prominent. The dependence of the quantum-interference effect on n{sup '} is predicted to be much weaker.« less

Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface.

PubMed

Löytynoja, T; Li, X; Jänkälä, K; Rinkevicius, Z; Ågren, H

2016-07-14

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface

NASA Astrophysics Data System (ADS)

Löytynoja, T.; Li, X.; Jänkälä, K.; Rinkevicius, Z.; Ågren, H.

2016-07-01

We study a newly devised quantum mechanics capacitance molecular mechanics (QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses.

PubMed

Baral, Khagendra; Li, Aize; Ching, Wai-Yim

2017-10-12

A density functional theory (DFT)-based ab initio molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li-Na and Na-K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li-O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations.

Formation of E-cyanomethamine in a nitrile rich environment

NASA Astrophysics Data System (ADS)

Shivani; Misra, Alka; Tandon, Poonam

2017-01-01

Recently a new molecule, cyanomethamine, has been detected towards Sagittarius B2(N) (Sgr B2(N)). Studying the formation mechanisms of complex interstellar molecules is difficult. Hence, a theoretical quantum chemical approach for analyzing the reaction mechanism describing the formation of interstellar cyanomethamine through detected interstellar molecules and radicals (NCCN+H) is discussed in the present work. Calculations are performed by using quantum chemical techniques, such as Density Functional Theory (DFT) and Møller-Plesset perturbation (MP2) theory with a 6-311G(d,p) basis set, both in the gas phase and in icy grains. The proposed reaction path (NCCN+H+H) has exothermicity with no barrier which indicates the possibility of cyanomethamine formation in the interstellar medium.

Reaction Mechanisms for the Electrochemical Reduction of CO 2 to CO and Formate on the Cu(100) Surface at 298 K from Quantum Mechanics Free Energy Calculations with Explicit Water

DOE PAGES

Cheng, Tao; Xiao, Hai; Goddard, William A.

2016-10-11

Copper is the only elemental metal that reduces a significant fraction of CO 2 to hydrocarbons and alcohols, but the atomistic reaction mechanism that controls the product distributions is not known because it has not been possible to detect the reaction intermediates on the electrode surface experimentally, or to carry out Quantum Mechanics (QM) calculations with a realistic description of the electrolyte (water). We carry out QM calculations with an explicit description of water on the Cu(100) surface (experimentally shown to be stable under CO 2 reduction reaction conditions) to examine the initial reaction pathways to form CO and formatemore » (HCOO –) from CO 2 through free energy calculations at 298 K and pH 7. We find that CO formation proceeds from physisorbed CO 2 to chemisorbed CO 2 (*CO 2 δ-), with a free energy barrier of ΔG ‡ = 0.43 eV, the rate-determining step (RDS). The subsequent barriers of protonating *CO 2 δ- to form COOH* and then dissociating COOH* to form *CO are 0.37 and 0.30 eV, respectively. HCOO– formation proceeds through a very different pathway in which physisorbed CO 2 reacts directly with a surface H* (along with electron transfer), leading to ΔG ‡ = 0.80 eV. Thus, the competition between CO formation and HCOO – formation occurs in the first electron-transfer step. On Cu(100), the RDS for CO formation is lower, making CO the predominant product. Therefore, to alter the product distribution, we need to control this first step of CO 2 binding, which might involve controlling pH, alloying, or changing the structure at the nanoscale.« less

Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

PubMed Central

Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo

2013-01-01

Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489

Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

PubMed

Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

2015-04-14

We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

NASA Astrophysics Data System (ADS)

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-01

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

Amino acid analogues bind to carbon nanotube via π-π interactions: comparison of molecular mechanical and quantum mechanical calculations.

PubMed

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-14

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

NIS, IR and Raman spectra with quantum mechanical calculations for analyzing the force field of hypericin model compounds

NASA Astrophysics Data System (ADS)

Ulicny, Jozef; Leulliot, Nicolas; Grajcar, Lydie; Baron, Marie-Hélène; Jobic, Hervé; Ghomi, Mahmoud

1999-06-01

Geometry optimization as well as harmonic force field calculations at HF and DFT levels of theory have been performed in order to elucidate the ground state properties of anthrone and emodin, two polycyclic conjugated molecules considered as hypericin model compounds. NIS, IR and FT-Raman spectra of these compounds have been recorded to validate the calculated results (geometry and vibrational modes). Calculated NIS spectra using the lowest energy conformers are in agreement with experiment. In addition, the intramolecular H-bonds in emodin predicted by the calculations can be evidenced using IR spectra as a function of temperature.

NIS, IR and Raman spectra with quantum mechanical calculations for analyzing the force field of hypericin model compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulicny, Jozef; Department of Biophysics, Safarik University, Jesenna 5, 04154 Kosice; Leulliot, Nicolas

1999-06-15

Geometry optimization as well as harmonic force field calculations at HF and DFT levels of theory have been performed in order to elucidate the ground state properties of anthrone and emodin, two polycyclic conjugated molecules considered as hypericin model compounds. NIS, IR and FT-Raman spectra of these compounds have been recorded to validate the calculated results (geometry and vibrational modes). Calculated NIS spectra using the lowest energy conformers are in agreement with experiment. In addition, the intramolecular H-bonds in emodin predicted by the calculations can be evidenced using IR spectra as a function of temperature.

Quantum Glass of Interacting Bosons with Off-Diagonal Disorder

NASA Astrophysics Data System (ADS)

Piekarska, A. M.; Kopeć, T. K.

2018-04-01

We study disordered interacting bosons described by the Bose-Hubbard model with Gaussian-distributed random tunneling amplitudes. It is shown that the off-diagonal disorder induces a spin-glass-like ground state, characterized by randomly frozen quantum-mechanical U(1) phases of bosons. To access criticality, we employ the "n -replica trick," as in the spin-glass theory, and the Trotter-Suzuki method for decomposition of the statistical density operator, along with numerical calculations. The interplay between disorder, quantum, and thermal fluctuations leads to phase diagrams exhibiting a glassy state of bosons, which are studied as a function of model parameters. The considered system may be relevant for quantum simulators of optical-lattice bosons, where the randomness can be introduced in a controlled way. The latter is supported by a proposition of experimental realization of the system in question.

Quantum Theory of Three-Dimensional Superresolution Using Rotating-PSF Imagery

NASA Astrophysics Data System (ADS)

Prasad, S.; Yu, Z.

The inverse of the quantum Fisher information (QFI) matrix (and extensions thereof) provides the ultimate lower bound on the variance of any unbiased estimation of a parameter from statistical data, whether of intrinsically quantum mechanical or classical character. We calculate the QFI for Poisson-shot-noise-limited imagery using the rotating PSF that can localize and resolve point sources fully in all three dimensions. We also propose an experimental approach based on the use of computer generated hologram and projective measurements to realize the QFI-limited variance for the problem of super-resolving a closely spaced pair of point sources at a highly reduced photon cost. The paper presents a preliminary analysis of quantum-limited three-dimensional (3D) pair optical super-resolution (OSR) problem with potential applications to astronomical imaging and 3D space-debris localization.

Quantum Crystallography: Density Matrix-Density Functional Theory and the X-Ray Diffraction Experiment

NASA Astrophysics Data System (ADS)

Soirat, Arnaud J. A.

Density Matrix Theory is a Quantum Mechanical formalism in which the wavefunction is eliminated and its role taken over by reduced density matrices. The interest of this is that, it allows one, in principle, to calculate any electronic property of a physical system, without having to solve the Schrodinger equation, using only two entities much simpler than an N-body wavefunction: first and second -order reduced density matrices. In practice, though, this very promising possibility faces the tremendous theoretical problem of N-representability, which has been solved for the former, but, until now, voids any hope of theoretically determining the latter. However, it has been shown that single determinant reduced density matrices of any order may be recovered from coherent X-ray diffraction data, if one provides a proper Quantum Mechanical description of the Crystallography experiment. A deeper investigation of this method is the purpose of this work, where we, first, further study the calculation of X-ray reduced density matrices N-representable by a single Slater determinant. In this context, we independently derive necessary and sufficient conditions for the uniqueness of the method. We then show how to account for electron correlation in this model. For the first time, indeed, we derive highly accurate, yet practical, density matrices approximately N-representable by correlated-determinant wavefunctions. The interest of such a result lies in the Quantum Mechanical validity of these density matrices, their property of being entirely obtainable from X-ray coherent diffraction data, their very high accuracy conferred by this known property of the N-representing wavefunction, as well as their definition as explicit functionals of the density. All of these properties are finally used in both a theoretical and a numerical application: in the former, we show that these density matrices may be used in the context of Density Functional Theory to highly accurately determine the unknown HK functional, associated with the theorem of Hohenberg and Kohn. The latter is provided by the calculation of helium correlation energy, where we test approximating the second-order density function by the leading term of its McLaurin's series expansion.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Quantum Mechanics for Beginning Physics Students

ERIC Educational Resources Information Center

Schneider, Mark B.

2010-01-01

The past two decades of attention to introductory physics education has emphasized enhanced development of conceptual understanding to accompany calculational ability. Given this, it is surprising that current texts continue to rely on the Bohr model to develop a flawed intuition, and introduce correct atomic physics on an ad hoc basis. For…

A molecular model for ice nucleation and growth, attachment 1

NASA Technical Reports Server (NTRS)

Plummer, P. L. M.

1981-01-01

The quantum mechanical technique is used to study ionic, configurational, and impurity defects in the ice surface. In addition to static calculations of the energetics of the water monomer-ice surface interactions, molecular dynamics studies were initiated. The calculations of the monomer-ice surface interaction, molecular dynamics studies were initiated. The calculations of monomer-ice surface interactions indicate that many adsorption sites exist on the ice surfaces and that the barriers between bonding sites are relatively low. Bonding on the prism face of ice is preferentially above lattice sites.

Hexagonal boron nitride and water interaction parameters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yanbin; Aluru, Narayana R., E-mail: aluru@illinois.edu; Wagner, Lucas K.

2016-04-28

The study of hexagonal boron nitride (hBN) in microfluidic and nanofluidic applications at the atomic level requires accurate force field parameters to describe the water-hBN interaction. In this work, we begin with benchmark quality first principles quantum Monte Carlo calculations on the interaction energy between water and hBN, which are used to validate random phase approximation (RPA) calculations. We then proceed with RPA to derive force field parameters, which are used to simulate water contact angle on bulk hBN, attaining a value within the experimental uncertainties. This paper demonstrates that end-to-end multiscale modeling, starting at detailed many-body quantum mechanics andmore » ending with macroscopic properties, with the approximations controlled along the way, is feasible for these systems.« less

Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies.

PubMed

Hansen, Katja; Montavon, Grégoire; Biegler, Franziska; Fazli, Siamac; Rupp, Matthias; Scheffler, Matthias; von Lilienfeld, O Anatole; Tkatchenko, Alexandre; Müller, Klaus-Robert

2013-08-13

The accurate and reliable prediction of properties of molecules typically requires computationally intensive quantum-chemical calculations. Recently, machine learning techniques applied to ab initio calculations have been proposed as an efficient approach for describing the energies of molecules in their given ground-state structure throughout chemical compound space (Rupp et al. Phys. Rev. Lett. 2012, 108, 058301). In this paper we outline a number of established machine learning techniques and investigate the influence of the molecular representation on the methods performance. The best methods achieve prediction errors of 3 kcal/mol for the atomization energies of a wide variety of molecules. Rationales for this performance improvement are given together with pitfalls and challenges when applying machine learning approaches to the prediction of quantum-mechanical observables.

Topics in quantum chaos

NASA Astrophysics Data System (ADS)

Jordan, Andrew Noble

2002-09-01

In this dissertation, we study the quantum mechanics of classically chaotic dynamical systems. We begin by considering the decoherence effects a quantum chaotic system has on a simple quantum few state system. Typical time evolution of a quantum system whose classical limit is chaotic generates structures in phase space whose size is much smaller than Planck's constant. A naive application of Heisenberg's uncertainty principle indicates that these structures are not physically relevant. However, if we take the quantum chaotic system in question to be an environment which interacts with a simple two state quantum system (qubit), we show that these small phase-space structures cause the qubit to generically lose quantum coherence if and only if the environment has many degrees of freedom, such as a dilute gas. This implies that many-body environments may be crucial for the phenomenon of quantum decoherence. Next, we turn to an analysis of statistical properties of time correlation functions and matrix elements of quantum chaotic systems. A semiclassical evaluation of matrix elements of an operator indicates that the dominant contribution will be related to a classical time correlation function over the energy surface. For a highly chaotic class of dynamics, these correlation functions may be decomposed into sums of Ruelle resonances, which control exponential decay to the ergodic distribution. The theory is illustrated both numerically and theoretically on the Baker map. For this system, we are able to isolate individual Ruelle modes. We further consider dynamical systems whose approach to ergodicity is given by a power law rather than an exponential in time. We propose a billiard with diffusive boundary conditions, whose classical solution may be calculated analytically. We go on to compare the exact solution with an approximation scheme, as well calculate asympotic corrections. Quantum spectral statistics are calculated assuming the validity of the Again, Altshuler and Andreev ansatz. We find singular behavior of the two point spectral correlator in the limit of small spacing. Finally, we analyse the effect that slow decay to ergodicity has on the structure of the quantum propagator, as well as wavefunction localization. We introduce a statistical quantum description of systems that are composed of both an orderly region and a random region. By averaging over the random region only, we find that measures of localization in momentum space semiclassically diverge with the dimension of the Hilbert space. We illustrate this numerically with quantum maps and suggest various other systems where this behavior should be important.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Formulation of D-brane Dynamics

NASA Astrophysics Data System (ADS)

Evans, Thomas

2012-03-01

It is the purpose of this paper (within the context of STS rules & guidelines ``research report'') to formulate a statistical-mechanical form of D-brane dynamics. We consider first the path integral formulation of quantum mechanics, and extend this to a path-integral formulation of D-brane mechanics, summing over all the possible path integral sectors of R-R, NS charged states. We then investigate this generalization utilizing a path-integral formulation summing over all the possible path integral sectors of R-R charged states, calculated from the mean probability tree-level amplitude of type I, IIA, and IIB strings, serving as a generalization of all strings described by D-branes. We utilize this generalization to study black holes in regimes where the initial D-brane system is legitimate, and further this generalization to look at information loss near regions of nonlocality on a non-ordinary event horizon. We see here that in these specific regimes, we can calculate a path integral formulation, as describing D0-brane mechanics, tracing the dissipation of entropy throughout the event horizon. This is used to study the information paradox, and to propose a resolution between the phenomena and the correct and expected quantum mechanical description. This is done as our path integral throughout entropy entering the event horizon effectively and correctly encodes the initial state in subtle correlations in the Hawking radiation.

Experimental and theoretical study of p-nitroacetanilide

NASA Astrophysics Data System (ADS)

Gnanasambandan, T.; Gunasekaran, S.; Seshadri, S.

2014-01-01

The spectroscopic properties of the p-nitroacetanilide (PNA) were examined by FT-IR, FT-Raman and UV-Vis techniques. FT-IR and FT-Raman spectra in solid state were observed in the region 4000-400 cm-1 and 3500-100 cm-1, respectively. The UV-Vis absorption spectrum of the compound that dissolved in ethanol was recorded in the range of 200-400 nm. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional theory (DFT) employing B3LYP methods with the 6-31G(d,p) and 6-311+G(d,p) basis sets. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear optical (NLO) properties such as electric dipole moment and first hyperpolarizability have been computed using B3LYP quantum chemical calculation.

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of ferulic acid by density functional study

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sundaraganesan, N.; Manoharan, S.

2009-10-01

Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of ferulic acid (FA) (4-hydroxy-3-methoxycinnamic acid) were carried out by using density functional (DFT/B3LYP/BLYP) method with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment ( μ) and the first hyperpolarizability ( β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the FA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of FA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT-IR and FT-Raman spectra for the title molecule have been constructed.

Electron energy can oscillate near a crystal dislocation

DOE PAGES

Li, Mingda; Cui, Wenping; Dresselhaus, Mildred S.; ...

2017-01-25

Crystal dislocations govern the plastic mechanical properties of materials but also affect the electrical and optical properties. However, a fundamental and quantitative quantum field theory of a dislocation has remained undiscovered for decades. Here in this article we present an exactly-solvable one-dimensional quantum field theory of a dislocation, for both edge and screw dislocations in an isotropic medium, by introducing a new quasiparticle which we have called the ‘dislon’. The electron-dislocation relaxation time can then be studied directly from the electron self-energy calculation, which is reducible to classical results. In addition, we predict that the electron energy will experience anmore » oscillation pattern near a dislocation. Compared with the electron density’s Friedel oscillation, such an oscillation is intrinsically different since it exists even with only single electron is present. With our approach, the effect of dislocations on materials’ non-mechanical properties can be studied at a full quantum field theoretical level.« less

Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

PubMed

Cendagorta, Joseph R; Powers, Anna; Hele, Timothy J H; Marsalek, Ondrej; Bačić, Zlatko; Tuckerman, Mark E

2016-11-30

Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H 2 and D 2 diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H 2 and D 2 as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H 2 and D 2 diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are strongly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as a result the quantum rate is greater than the classical rate.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Combined Monte Carlo and quantum mechanics study of the solvatochromism of phenol in water. The origin of the blue shift of the lowest pi-pi* transition.

PubMed

Barreto, Rafael C; Coutinho, Kaline; Georg, Herbert C; Canuto, Sylvio

2009-03-07

A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is made to analyze the spectral shift of the lowest pi-pi* transition of phenol in water. The solute polarization is included using electrostatic embedded calculations at the MP2/aug-cc-pVDZ level giving a dipole moment of 2.25 D, corresponding to an increase of 76% compared to the calculated gas-phase value. Using statistically uncorrelated configurations sampled from the MC simulation, first-principle size-extensive calculations are performed to obtain the solvatochromic shift. Analysis is then made of the origin of the blue shift. Results both at the optimized geometry and in room-temperature liquid water show that hydrogen bonds of water with phenol promote a red shift when phenol is the proton-donor and a blue shift when phenol is the proton-acceptor. In the case of the optimized clusters the calculated shifts are in very good agreement with results obtained from mass-selected free jet expansion experiments. In the liquid case the contribution of the solute-solvent hydrogen bonds partially cancels and the total shift obtained is dominated by the contribution of the outer solvent water molecules. Our best result, including both inner and outer water molecules, is 570 +/- 35 cm(-1), in very good agreement with the small experimental shift of 460 cm(-1) for the absorption maximum.

A comparative experimental and quantum chemical study on monomeric and dimeric structures of 3,5-dibromoanthranilic acid.

PubMed

Karabacak, Mehmet; Cinar, Mehmet

2012-10-01

This study presents the structural and spectroscopic characterization of 3,5-dibromoanthranilic acid with help of experimental techniques (FT-IR, FT-Raman, UV, NMR) and quantum chemical calculations. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman in the range of 4000-400 and 4000-50 cm(-1), respectively. The vibrational frequencies were also computed using B3LYP method of DFT with 6-311++G(d,p) basis set. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The (1)H, (13)C and DEPT NMR spectra were recorded in DMSO solution and calculated by gauge-invariant atomic orbitals (GIAO) method. The UV absorption spectra of the compound were recorded in the range of 200-400 nm in ethanol, water and DMSO solutions. Solvent effects were calculated using time-dependent density functional theory and CIS method. The ground state geometrical structure of compound was predicted by B3LYP method and compared with the crystallographic structure of similar compounds. All calculations were made for monomeric and dimeric structure of compound. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken atomic charges of neutral and anionic form of the molecule were computed and compared with anthranilic acid. Copyright © 2012 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xiaoyao; Hall, Randall W.; Löffler, Frank

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H2O, N2, and F2 molecules. The method is based on Feynman’s path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of other quantum chemical methodsmore » and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.« less

Relativistic entanglement

NASA Astrophysics Data System (ADS)

Horwitz, Lawrence; Arshansky, Rafael I.

2018-07-01

The relativistic quantum theory of Stueckelberg, Horwitz and Piron (SHP) describes in a simple way the experiment on interference in time of an electron emitted by femtosecond laser pulses carried out by Lindner et al. In this paper, we show that, in a way similar to our study of the Lindner et al. experiment (with some additional discussion of the covariant quantum mechanical description of spin and angular momentum), the experiment proposed by Palacios et al. to demonstrate entanglement of a two electron state, where the electrons are separated in time of emission, has a consistent interpretation in terms of the SHP theory. We find, after a simple calculation, results in essential agreement with those of Palacios et al.; but with the observed times as values of proper quantum observables.

Interdot spacing dependence of electronic structure and properties of multistacked InGaAs quantum dots fabricated without strain compensation technique

NASA Astrophysics Data System (ADS)

Goshima, Keishiro; Tsuda, Norio; Inukai, Keisuke; Amano, Takeru; Sugaya, Takeyoshi

2018-06-01

We report on the electronic properties and band structure of multistacked quantum dots (QDs) fabricated without a strain compensation technique. It is possible to realize a small interdot spacing and introduce a strong quantum mechanical coupling. From the using temperature dependence, polarized photoluminescent spectra, and photoluminescent excitation experiments, we observe a markedly different behavior depending on the interdot spacing. These results evidence that minibands of electrons and holes are formed with interdot spacings of 7 and 3.5 nm, respectively. In addition, thise results are in good agreement with numerical calculations. We describe in detail the miniband formation and electronic structure of multistacked QDs with various interdot spacings of 10 nm or less.

Electronic transport in a long wavelength infrared quantum cascade detector under dark condition

NASA Astrophysics Data System (ADS)

Li, L.; Zhou, X. H.; Lin, T.; Li, N.; Zhu, Z. Q.; Liu, F. Q.

2016-09-01

We present a joint experimental and theoretical investigation on a long wavelength infrared quantum cascade detector to reveal its dark current paths. The temperature dependence of the dark current is measured. It is shown that there are two different transport mechanisms, namely resonant tunneling at low temperatures and thermal excitation at higher temperature, dominate the carrier flow, respectively. Moreover, the experimental intersubband transition energies obtained by the magneto-transport measurements matches the theoretical predictions well. With the aid of the calculated band structures, we can explain the observed oscillation phenomena of the dark current under the magnetic field very well. The obtained results provide insight into the transport properties of quantum cascade detectors thus providing a useful tool for device optimization.

Optical model analyses of galactic cosmic ray fragmentation in hydrogen targets

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.

1993-01-01

Quantum-mechanical optical model methods for calculating cross sections for the fragmentation of galactic cosmic ray nuclei by hydrogen targets are presented. The fragmentation cross sections are calculated with an abrasion-ablation collision formalism. Elemental and isotopic cross sections are estimated and compared with measured values for neon, sulfur, and calcium ions at incident energies between 400A MeV and 910A MeV. Good agreement between theory and experiment is obtained.

Quantum mechanical study and spectroscopic (FT-IR, FT-Raman, 13C, 1H) study, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of 2-acetoxybenzoic acid by density functional methods

NASA Astrophysics Data System (ADS)

Bhavani, K.; Renuga, S.; Muthu, S.; Sankara narayanan, K.

2015-02-01

In this work, colorless crystals of 2-acetoxybenzoic acid were grown by slow evaporation method and the FT-IR and FT-Raman spectra of the sample were recorded in the region 4000-500 cm-1 and 4000-100 cm-1 respectively. Molecular structure is optimized with the help of density functional theory method (B3LYP) with 6-31+G(d,p), 6-311++G(d,p) basis sets. Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the σ∗ antibonding orbitals and E(2) energies confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis following the scaled quantum mechanical force field (SQMFF) methodology. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. Mulliken population analysis on atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule.

Target electron collision effects on energy loss straggling of protons in an electron gas at any degeneracy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barriga-Carrasco, Manuel D.

2008-03-15

The purpose of the present paper is to describe the effects of target electron collisions on proton energy loss straggling in plasmas at any degeneracy. Targets are considered fully ionized so electronic energy loss is only due to the free electrons. The analysis is focused on targets with electronic density around solid values n{sub e}{approx_equal}10{sup 23} cm{sup -3} and with temperature around T{approx_equal}10 eV; these targets are in the limit of weakly coupled electron gases. These types of plasma targets have not been studied extensively, though they are very important for inertial confinement fusion. The energy loss straggling is obtainedmore » from an exact quantum-mechanical evaluation, which takes into account the degeneracy of the target plasma, and later it is compared with common classical and degenerate approximations. Then electron collisions in the exact quantum-mechanical straggling calculation are considered. Now the energy loss straggling is enhanced for energies smaller than the energy before the maximum, then decreases around this maximum, and finally tends to the same values with respect to noncollisional calculation. Differences with the same results but not taking into account these collisions are as far as 17% in the cases analyzed. As an example, proton range distributions have been calculated to show the importance of an accurate energy straggling calculation.« less

Quantum communication for satellite-to-ground networks with partially entangled states

NASA Astrophysics Data System (ADS)

Chen, Na; Quan, Dong-Xiao; Pei, Chang-Xing; Yang-Hong

2015-02-01

To realize practical wide-area quantum communication, a satellite-to-ground network with partially entangled states is developed in this paper. For efficiency and security reasons, the existing method of quantum communication in distributed wireless quantum networks with partially entangled states cannot be applied directly to the proposed quantum network. Based on this point, an efficient and secure quantum communication scheme with partially entangled states is presented. In our scheme, the source node performs teleportation only after an end-to-end entangled state has been established by entanglement swapping with partially entangled states. Thus, the security of quantum communication is guaranteed. The destination node recovers the transmitted quantum bit with the help of an auxiliary quantum bit and specially defined unitary matrices. Detailed calculations and simulation analyses show that the probability of successfully transferring a quantum bit in the presented scheme is high. In addition, the auxiliary quantum bit provides a heralded mechanism for successful communication. Based on the critical components that are presented in this article an efficient, secure, and practical wide-area quantum communication can be achieved. Project supported by the National Natural Science Foundation of China (Grant Nos. 61072067 and 61372076), the 111 Project (Grant No. B08038), the Fund from the State Key Laboratory of Integrated Services Networks (Grant No. ISN 1001004), and the Fundamental Research Funds for the Central Universities (Grant Nos. K5051301059 and K5051201021).

Thermal, dielectric characteristics and conduction mechanism of azodyes derived from quinoline and their copper complexes.

PubMed

El-Ghamaz, N A; Diab, M A; El-Bindary, A A; El-Sonbati, A Z; Nozha, S G

2015-05-15

A novel series of (5-(4'-derivatives phenyl azo)-8-hydroxy-7-quinolinecarboxaldehyde) (AQLn) (n=1, p-OCH3; n=2, R=H; and n=3; p-NO2) and their complexes [Cu(AQLn)2]·5H2O are synthesized and investigated. The optimized bond lengths, bond angles and the calculated quantum chemical parameters for AQLn are investigated. HOMO-LUMO energy gap, absolute electronegativities, chemical potentials, and absolute hardness are also calculated. The thermal properties, dielectric properties, alternating current conductivity (σac) and conduction mechanism are investigated in the frequency range 0.1-100kHz and temperature range 293-568K for AQL1-3 and 318-693K for [Cu(AQL1-3)2]·5H2O complexes. The thermal properties are of ligands (AQLn) and their Cu(II) complexes investigated by thermogravimetric analysis (TGA). The temperature and frequency dependence of the real and the imaginary part of the dielectric constant are studied. The values of the thermal activation energy of conduction mechanism for AQLn and their complexes [Cu(AQLn)2]·5H2O under investigation are calculated at different test frequencies. The values of thermal activation energies ΔE1 and ΔE2 for AQLn and [Cu(AQLn)2]·5H2O decrease with increasing the values of frequency. The ac conductivity is found to be depending on the chemical structure of the compounds. Different conduction mechanisms have been proposed to explain the obtained experimental data. The small polaron tunneling (SPT) is the dominant conduction mechanism for AQL1 and its complex [Cu(AQL1)2]·5H2O. The quantum mechanical tunneling (QMT) is the dominant conduction mechanism for AQL2 and its complex [Cu(AQL2)2]·5H2O. The correlated barrier hopping (CBH) is the dominant conduction mechanism for AQL3 and its complex [Cu(AQL3)2]·5H2O, and the values of the maximum barrier height (Wm) are calculated. Copyright © 2015 Elsevier B.V. All rights reserved.

The measurement problem in quantum mechanics: A phenomenological investigation

NASA Astrophysics Data System (ADS)

Hunter, Joel Brooks

2008-10-01

This dissertation is a phenomenological investigation of the measurement problem in quantum mechanics. The primary subject matter for description and analysis is scientific instruments and their use in experiments which elicit the measurement problem. A methodological critique is mounted against the ontological commitments taken for granted in the canonical interpretations of quantum theory and the scientific activity of measurement as the necessary interface between theoretical interest and perceptual results. I argue that an aesthetic dimension of reality functions as aproto-scientific establishment of sense-making that constantly operates to set integratively all other cognitively neat determinations, including scientifically rendered objects that are intrinsically non-visualizable. The way in which data "key in" to the original and originative register of the sensible in observation is clarified by examining prostheses, measuring apparatuses and instruments that are sense-conveying and -integrative with the human sensorium. Experiments, technology and instrumentation are examined in order to understand how knowing and that which is known is bonded by praxis-aisthesis. Quantum measurement is a praxic-dynamie activity and homologically structured and structur ing functional engagement in terms of instantiation, quantifiability, and spatiotemporal differentiation. The distinctions between a beauty-aesthetic and praxis-aisthesis are delineated. It is argued that a beauty-aesthetic is a construal of the economic dimension of scientific objects and work, and is not the primary manner in which the aesthetic dimension is disclosed. The economic dimension of abstractions reduces to an austere aesthetic of calculative economy. Nature itself, however, is not stingy; it is intrinsically capacious, extravagant, full of surprise, nuance, ambiguity and allusiveness. The capaciousness of Nature and the way in which we are integratively set within Nature in a materiality-phenomenality correlation discloses Nature's constituent potential, a condition more primitive than causal interplay. Finally, the relation between a physical mechanism or process and its functional mathematical representation is clarified. No physical mechanism or process accounts for the empirical effects of measurement outcomes in some quantum mechanical experiments. Within the milieu of ordinary perceptual experience, complete with its horizonal structure of spatiality and temporality, something uncaused is encountered which resists full determination in terms of mathematical representation. Keywords: Quantum Mechanics, Measurement Problem, Phenomenology, Prosthesis, Aesthetic

Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries.

PubMed

Brorsen, Kurt R; Yang, Yang; Hammes-Schiffer, Sharon

2017-08-03

Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear-electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron-proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron-proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF - . The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pK a 's, optimized geometries, and reaction paths.

Entanglement in Nonunitary Quantum Critical Spin Chains

NASA Astrophysics Data System (ADS)

Couvreur, Romain; Jacobsen, Jesper Lykke; Saleur, Hubert

2017-07-01

Entanglement entropy has proven invaluable to our understanding of quantum criticality. It is natural to try to extend the concept to "nonunitary quantum mechanics," which has seen growing interest from areas as diverse as open quantum systems, noninteracting electronic disordered systems, or nonunitary conformal field theory (CFT). We propose and investigate such an extension here, by focusing on the case of one-dimensional quantum group symmetric or supergroup symmetric spin chains. We show that the consideration of left and right eigenstates combined with appropriate definitions of the trace leads to a natural definition of Rényi entropies in a large variety of models. We interpret this definition geometrically in terms of related loop models and calculate the corresponding scaling in the conformal case. This allows us to distinguish the role of the central charge and effective central charge in rational minimal models of CFT, and to define an effective central charge in other, less well-understood cases. The example of the s l (2 |1 ) alternating spin chain for percolation is discussed in detail.

Polarized electron beams elastically scattered by atoms as a tool for testing fundamental predictions of quantum mechanics.

PubMed

Dapor, Maurizio

2018-03-29

Quantum information theory deals with quantum noise in order to protect physical quantum bits (qubits) from its effects. A single electron is an emblematic example of a qubit, and today it is possible to experimentally produce polarized ensembles of electrons. In this paper, the theory of the polarization of electron beams elastically scattered by atoms is briefly summarized. Then the POLARe program suite, a set of computer programs aimed at the calculation of the spin-polarization parameters of electron beams elastically interacting with atomic targets, is described. Selected results of the program concerning Ar, Kr, and Xe atoms are presented together with the comparison with experimental data about the Sherman function for low kinetic energy of the incident electrons (1.5eV-350eV). It is demonstrated that the quantum-relativistic theory of the polarization of electron beams elastically scattered by atoms is in good agreement with experimental data down to energies smaller than a few eV.

Can quantum coherent solar cells break detailed balance?

NASA Astrophysics Data System (ADS)

Kirk, Alexander P.

2015-07-01

Carefully engineered coherent quantum states have been proposed as a design attribute that is hypothesized to enable solar photovoltaic cells to break the detailed balance (or radiative) limit of power conversion efficiency by possibly causing radiative recombination to be suppressed. However, in full compliance with the principles of statistical mechanics and the laws of thermodynamics, specially prepared coherent quantum states do not allow a solar photovoltaic cell—a quantum threshold energy conversion device—to exceed the detailed balance limit of power conversion efficiency. At the condition given by steady-state open circuit operation with zero nonradiative recombination, the photon absorption rate (or carrier photogeneration rate) must balance the photon emission rate (or carrier radiative recombination rate) thus ensuring that detailed balance prevails. Quantum state transitions, entropy-generating hot carrier relaxation, and photon absorption and emission rate balancing are employed holistically and self-consistently along with calculations of current density, voltage, and power conversion efficiency to explain why detailed balance may not be violated in solar photovoltaic cells.

Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

Crossover to the anomalous quantum regime in the extrinsic spin Hall effect of graphene

NASA Astrophysics Data System (ADS)

Ferreira, Aires; Milletari, Mirco

Recent reports of spin-orbit coupling enhancement in chemically modified graphene have opened doors to studies of the spin Hall effect with massless chiral fermions. Here, we theoretically investigate the interaction and impurity density dependence of the extrinsic spin Hall effect in spin-orbit coupled graphene. We present a nonperturbative quantum diagrammatic calculation of the spin Hall response function in the strong-coupling regime that incorporates skew scattering and anomalous impurity density-independent contributions on equal footing. The spin Hall conductivity dependence on Fermi energy and electron-impurity interaction strength reveals the existence of experimentally accessible regions where anomalous quantum processes dominate. Our findings suggest that spin-orbit-coupled graphene is an ideal model system for probing the competition between semiclassical and bona fide quantum scattering mechanisms underlying the spin Hall effect. A.F. gratefully acknowledges the financial support of the Royal Society (U.K.).

Particle detection and non-detection in a quantum time of arrival measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sombillo, Denny Lane B., E-mail: dsombillo@nip.upd.edu.ph; Galapon, Eric A.

2016-01-15

The standard time-of-arrival distribution cannot reproduce both the temporal and the spatial profile of the modulus squared of the time-evolved wave function for an arbitrary initial state. In particular, the time-of-arrival distribution gives a non-vanishing probability even if the wave function is zero at a given point for all values of time. This poses a problem in the standard formulation of quantum mechanics where one quantizes a classical observable and uses its spectral resolution to calculate the corresponding distribution. In this work, we show that the modulus squared of the time-evolved wave function is in fact contained in one ofmore » the degenerate eigenfunctions of the quantized time-of-arrival operator. This generalizes our understanding of quantum arrival phenomenon where particle detection is not a necessary requirement, thereby providing a direct link between time-of-arrival quantization and the outcomes of the two-slit experiment. -- Highlights: •The time-evolved position density is contained in the standard TOA distribution. •Particle may quantum mechanically arrive at a given point without being detected. •The eigenstates of the standard TOA operator are linked to the two-slit experiment.« less

Quantum close coupling calculation of transport and relaxation properties for Hg-H2 system

NASA Astrophysics Data System (ADS)

Nemati-Kande, Ebrahim; Maghari, Ali

2016-11-01

Quantum mechanical close coupling calculation of the state-to-state transport and relaxation cross sections have been done for Hg-H2 molecular system using a high-level ab initio potential energy surface. Rotationally averaged cross sections were also calculated to obtain the energy dependent Senftleben-Beenakker cross sections at the energy range of 0.005-25,000 cm-1. Boltzmann averaging of the energy dependent Senftleben-Beenakker cross sections showed the temperature dependency over a wide temperature range of 50-2500 K. Interaction viscosity and diffusion coefficients were also calculated using close coupling cross sections and full classical Mason-Monchick approximation. The results were compared with each other and with the available experimental data. It was found that Mason-Monchick approximation for viscosity is more reliable than diffusion coefficient. Furthermore, from the comparison of the experimental diffusion coefficients with the result of the close coupling and Mason-Monchick approximation, it was found that the Hg-H2 potential energy surface used in this work can reliably predict diffusion coefficient data.

Quantum electron tunneling in respiratory complex I.

PubMed

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A

2011-05-12

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. While the one-electron tunneling approximation is found to hold in electron tunneling between the antiferromagnetic binuclear and tetranuclear Fe/S clusters without major orbital or spin rearrangement of the core electrons, induced polarization of the core electrons contributes significantly to decrease the electron transfer rates to 19-56 %. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of the electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A signature of the wave properties of electrons is observed as distinct quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included is in good agreement with a reported phenomenological relation.

Argentate(i) and (iii) complexes as intermediates in silver-mediated cross-coupling reactions.

PubMed

Weske, Sebastian; Hardin, Richard A; Auth, Thomas; O'Hair, Richard A J; Koszinowski, Konrad; Ogle, Craig A

2018-04-30

Despite the potential of silver to mediate synthetically valuable cross-coupling reactions, the operating mechanisms have remained unknown. Here, we use a combination of rapid-injection NMR spectroscopy, electrospray-ionization mass spectrometry, and quantum chemical calculations to demonstrate that these transformations involve argentate(i) and (iii) complexes as key intermediates.

Predicting charmonium and bottomonium spectra with a quark harmonic oscillator.

PubMed

Norbury, J W; Badavi, F F; Townsend, L W

1986-11-01

We present a simple application of the three-dimensional harmonic oscillator which should provide a very nice particle physics example to be presented in introductory undergraduate quantum mechanics course. The idea is to use the nonrelativistic quark model to calculate the spin-averaged mass levels of the charmonium and bottomonium spectra.

Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

ERIC Educational Resources Information Center

Halpern, Arthur M.

2011-01-01

A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

Proceedings: Conference on Computers in Chemical Education and Research, Dekalb, Illinois, 19-23 July 1971.

ERIC Educational Resources Information Center

1971

Computers have effected a comprehensive transformation of chemistry. Computers have greatly enhanced the chemist's ability to do model building, simulations, data refinement and reduction, analysis of data in terms of models, on-line data logging, automated control of experiments, quantum chemistry and statistical and mechanical calculations, and…

Quantum chemical approaches in structure-based virtual screening and lead optimization

NASA Astrophysics Data System (ADS)

Cavasotto, Claudio N.; Adler, Natalia S.; Aucar, Maria G.

2018-05-01

Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due to methodological developments and to the enormous advance in computer hardware, methods based on quantum mechanics (QM) have gained great attention in the last 10 years, and calculations on biomacromolecules are becoming increasingly explored, aiming to provide better accuracy in the description of protein-ligand interactions and the prediction of binding affinities. In principle, the QM formulation includes all contributions to the energy, accounting for terms usually missing in molecular mechanics force-fields, such as electronic polarization effects, metal coordination, and covalent binding; moreover, QM methods are systematically improvable, and provide a greater degree of transferability. In this mini-review we present recent applications of explicit QM-based methods in small-molecule docking and scoring, and in the calculation of binding free-energy in protein-ligand systems. Although the routine use of QM-based approaches in an industrial drug lead discovery setting remains a formidable challenging task, it is likely they will increasingly become active players within the drug discovery pipeline.

Undergraduate quantum mechanics: lost opportunities for engaging motivated students?

NASA Astrophysics Data System (ADS)

Johansson, Anders

2018-03-01

Quantum mechanics is widely recognised as an important and difficult subject, and many studies have been published focusing on students’ conceptual difficulties. However, the sociocultural aspects of studying such an emblematic subject have not been researched to any large extent. This study explores students’ experiences of undergraduate quantum mechanics using qualitative analysis of semi-structured interview data. The results inform discussions about the teaching of quantum mechanics by adding a sociocultural dimension. Students pictured quantum mechanics as an intriguing subject that inspired them to study physics. The study environment they encountered when taking their first quantum mechanics course was however not always as inspiring as expected. Quantum mechanics instruction has commonly focused on the mathematical framework of quantum mechanics, and this kind of teaching was also what the interviewees had experienced. Two ways of handling the encounter with a traditional quantum mechanics course were identified in the interviews; either students accept the practice of studying quantum mechanics in a mathematical, exercise-centred way or they distance themselves from these practices and the subject. The students who responded by distancing themselves experienced a crisis and disappointment, where their experiences did not match the way they imagined themselves engaging with quantum mechanics. The implications of these findings are discussed in relation to efforts to reform the teaching of undergraduate quantum mechanics.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

PubMed

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-05

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins

NASA Astrophysics Data System (ADS)

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-01

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Jeremy C; Bondar, A.N.; Suhai, Sandor

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 ofmore » 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.« less

The Contradiction Between the Measurement Theory of Quantum Mechanics and the Theory that the Velocity of Any Particle Can Not be Larger than the Velocity of Light

NASA Technical Reports Server (NTRS)

Shen, Y.; Shen, Z. J.; Shen, G. T.; Yang, B. C.

1996-01-01

By the measurement theory of quantum mechanics and the method of Fourier transform,we proved that the wave function psi(x,y,z,t)= (8/((2(pi)(2L(exp (1/2)))(exp 3))(Phi(L,t,x)Phi(L,t,y)Phi(L,t,z)). According to the theory that the velocity of any particle can not be larger than the velocity of light and the Born interpretation, when absolute value of delta greater than (ct+ L),Phi(L,t,delta) = 0. But according to the calculation, we proved that for some delta, even if absolute value of delta is greater than (ct+L), Phi(L,t,delta) is not equal to 0.

Thermal and Quantum Mechanical Noise of a Superfluid Gyroscope

NASA Technical Reports Server (NTRS)

Chui, Talso; Penanen, Konstantin

2004-01-01

A potential application of a superfluid gyroscope is for real-time measurements of the small variations in the rotational speed of the Earth, the Moon, and Mars. Such rotational jitter, if not measured and corrected for, will be a limiting factor on the resolution potential of a GPS system. This limitation will prevent many automation concepts in navigation, construction, and biomedical examination from being realized. We present the calculation of thermal and quantum-mechanical phase noise across the Josephson junction of a superfluid gyroscope. This allows us to derive the fundamental limits on the performance of a superfluid gyroscope. We show that the fundamental limit on real-time GPS due to rotational jitter can be reduced to well below 1 millimeter/day. Other limitations and their potential mitigation will also be discussed.

Deformed supersymmetric quantum mechanics with spin variables

NASA Astrophysics Data System (ADS)

Fedoruk, Sergey; Ivanov, Evgeny; Sidorov, Stepan

2018-01-01

We quantize the one-particle model of the SU(2|1) supersymmetric multiparticle mechanics with the additional semi-dynamical spin degrees of freedom. We find the relevant energy spectrum and the full set of physical states as functions of the mass-dimension deformation parameter m and SU(2) spin q\\in (Z_{>0,}1/2+Z_{≥0}) . It is found that the states at the fixed energy level form irreducible multiplets of the supergroup SU(2|1). Also, the hidden superconformal symmetry OSp(4|2) of the model is revealed in the classical and quantum cases. We calculate the OSp(4|2) Casimir operators and demonstrate that the full set of the physical states belonging to different energy levels at fixed q are unified into an irreducible OSp(4|2) multiplet.

Explicit polarization: a quantum mechanical framework for developing next generation force fields.

PubMed

Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel

2014-09-16

Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis.

Dynamical importance of van der Waals saddle and excited potential surface in C(1D)+D2 complex-forming reaction

PubMed Central

Shen, Zhitao; Ma, Haitao; Zhang, Chunfang; Fu, Mingkai; Wu, Yanan; Bian, Wensheng; Cao, Jianwei

2017-01-01

Encouraged by recent advances in revealing significant effects of van der Waals wells on reaction dynamics, many people assume that van der Waals wells are inevitable in chemical reactions. Here we find that the weak long-range forces cause van der Waals saddles in the prototypical C(1D)+D2 complex-forming reaction that have very different dynamical effects from van der Waals wells at low collision energies. Accurate quantum dynamics calculations on our highly accurate ab initio potential energy surfaces with van der Waals saddles yield cross-sections in close agreement with crossed-beam experiments, whereas the same calculations on an earlier surface with van der Waals wells produce much smaller cross-sections at low energies. Further trajectory calculations reveal that the van der Waals saddle leads to a torsion then sideways insertion reaction mechanism, whereas the well suppresses reactivity. Quantum diffraction oscillations and sharp resonances are also predicted based on our ground- and excited-state potential energy surfaces. PMID:28094253

Ab initio quantum mechanical calculation of the reaction probability for the Cl-+PH2Cl→ClPH2+Cl- reaction

NASA Astrophysics Data System (ADS)

Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.

2013-11-01

The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

Improved techniques for outgoing wave variational principle calculations of converged state-to-state transition probabilities for chemical reactions

NASA Technical Reports Server (NTRS)

Mielke, Steven L.; Truhlar, Donald G.; Schwenke, David W.

1991-01-01

Improved techniques and well-optimized basis sets are presented for application of the outgoing wave variational principle to calculate converged quantum mechanical reaction probabilities. They are illustrated with calculations for the reactions D + H2 yields HD + H with total angular momentum J = 3 and F + H2 yields HF + H with J = 0 and 3. The optimization involves the choice of distortion potential, the grid for calculating half-integrated Green's functions, the placement, width, and number of primitive distributed Gaussians, and the computationally most efficient partition between dynamically adapted and primitive basis functions. Benchmark calculations with 224-1064 channels are presented.

Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2004-01-01

We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene II. 3,3-Dimethyl-1,2-bis(trimethylsilyl)cyclopropene

NASA Astrophysics Data System (ADS)

Panchenko, Yu. N.; De Maré, G. R.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2003-07-01

The IR and Raman spectra of 3,3-dimethyl-1,2-bis(trimethylsilyl)cyclopropene (I) (synthesised using standard procedures) were measured in the liquid phase. Total geometry optimisation was performed at the HF/6-31G* level. The HF/6-31G*//HF/6-31G* quantum mechanical force field (QMFF) was calculated and used to determine the theoretical fundamental vibrational frequencies, their predicted IR intensities, Raman activities, and Raman depolarisation ratios. Using Pulay's scaling method and the theoretical molecular geometry, the QMFF of I was scaled by a set of scaling factors used previously for 3,3-dimethyl-1,2-bis(tert-butyl)cyclopropene (17 scale factors for a 105-dimensional problem). The scaled QMFF obtained was used to solve the vibrational problem. The quantum mechanical values of the Raman activities were converted to differential Raman cross sections. The figures for the experimental and theoretical Raman and IR spectra are presented. Assignments of the experimental vibrational spectra of I are given. They take into account the calculated potential energy distribution and the correlation between the estimations of the experimental IR and Raman intensities and Raman depolarisation ratios and the corresponding theoretical values (including Raman cross sections) calculated using the unscaled QMFF.

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

PubMed Central

Send, Robert; Kaila, Ville R. I.; Sundholm, Dage

2011-01-01

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV . By using a RVS energy threshold of 50 eV , the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2∕TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics∕molecular mechanics separation schemes. PMID:21663351

Spiers Memorial Lecture. Quantum chemistry: the first seventy years.

PubMed

McWeeny, Roy

2007-01-01

Present-day theoretical chemistry is rooted in Quantum Mechanics. The aim of the opening lecture is to trace the evolution of Quantum Chemistry from the Heitler-London paper of 1927 up to the end of the last century, emphasizing concepts rather than calculations. The importance of symmetry concepts became evident in the early years: one thinks of the necessary anti-symmetry of the wave function under electron permutations, the Pauli principle, the aufbau scheme, and the classification of spectroscopic states. But for chemists perhaps the key concept is embodied in the Hellmann-Feynman theorem, which provides a pictorial interpretation of chemical bonding in terms of classical electrostatic forces exerted on the nuclei by the electron distribution. Much of the lecture is concerned with various electron distribution functions--the electron density, the current density, the spin density, and other 'property densities'--and with their use in interpreting both molecular structure and molecular properties. Other topics touched upon include Response theory and propagators; Chemical groups in molecules and the group function approach; Atoms in molecules and Bader's theory; Electron correlation and the 'pair function'. Finally, some long-standing controversies, in particular the EPR paradox, are re-examined in the context of molecular dissociation. By admitting the concept of symmetry breaking, along with the use of the von Neumann-Dirac statistical ensemble, orthodox quantum mechanics can lead to a convincing picture of the dissociation mechanism.

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Engel, Edgar A., E-mail: eae32@cam.ac.uk; Needs, Richard J.; Monserrat, Bartomeu

Surface energies of hexagonal and cubic water ice are calculated using first-principles quantum mechanical methods, including an accurate description of anharmonic nuclear vibrations. We consider two proton-orderings of the hexagonal and cubic ice basal surfaces and three proton-orderings of hexagonal ice prism surfaces, finding that vibrations reduce the surface energies by more than 10%. We compare our vibrational densities of states to recent sum frequency generation absorption measurements and identify surface proton-orderings of experimental ice samples and the origins of characteristic absorption peaks. We also calculate zero point quantum vibrational corrections to the surface electronic band gaps, which range frommore » −1.2 eV for the cubic ice basal surface up to −1.4 eV for the hexagonal ice prism surface. The vibrational corrections to the surface band gaps are up to 12% smaller than for bulk ice.« less

Sum rules for zeros and intersections of Bessel functions from quantum mechanical perturbation theory

NASA Astrophysics Data System (ADS)

Pedersen, Thomas Garm

2018-07-01

Bessel functions play an important role for quantum states in spherical and cylindrical geometries. In cases of perfect confinement, the energy of Schrödinger and massless Dirac fermions is determined by the zeros and intersections of Bessel functions, respectively. In an external electric field, standard perturbation theory therefore expresses the polarizability as a sum over these zeros or intersections. Both non-relativistic and relativistic polarizabilities can be calculated analytically, however. Hence, by equating analytical expressions to perturbation expansions, several sum rules for the zeros and intersections of Bessel functions emerge.

High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K

NASA Astrophysics Data System (ADS)

Nguyen, Thanh Lam; Stanton, John F.

2017-10-01

Hydrogen abstraction from NH3 by OH to produce H2O and NH2—an important reaction in combustion of NH3 fuel—was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5%-20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K.

PubMed

Nguyen, Thanh Lam; Stanton, John F

2017-10-21

Hydrogen abstraction from NH 3 by OH to produce H 2 O and NH 2 -an important reaction in combustion of NH 3 fuel-was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5%-20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

General properties of the Foldy-Wouthuysen transformation and applicability of the corrected original Foldy-Wouthuysen method

NASA Astrophysics Data System (ADS)

Silenko, Alexander J.

2016-02-01

General properties of the Foldy-Wouthuysen transformation which is widely used in quantum mechanics and quantum chemistry are considered. Merits and demerits of the original Foldy-Wouthuysen transformation method are analyzed. While this method does not satisfy the Eriksen condition of the Foldy-Wouthuysen transformation, it can be corrected with the use of the Baker-Campbell-Hausdorff formula. We show a possibility of such a correction and propose an appropriate algorithm of calculations. An applicability of the corrected Foldy-Wouthuysen method is restricted by the condition of convergence of a series of relativistic corrections.

Effective numerical method of spectral analysis of quantum graphs

NASA Astrophysics Data System (ADS)

Barrera-Figueroa, Víctor; Rabinovich, Vladimir S.

2017-05-01

We present in the paper an effective numerical method for the determination of the spectra of periodic metric graphs equipped by Schrödinger operators with real-valued periodic electric potentials as Hamiltonians and with Kirchhoff and Neumann conditions at the vertices. Our method is based on the spectral parameter power series method, which leads to a series representation of the dispersion equation, which is suitable for both analytical and numerical calculations. Several important examples demonstrate the effectiveness of our method for some periodic graphs of interest that possess potentials usually found in quantum mechanics.

Impurity-induced tuning of quantum-well States in spin-dependent resonant tunneling.

PubMed

Kalitsov, Alan; Coho, A; Kioussis, Nicholas; Vedyayev, Anatoly; Chshiev, M; Granovsky, A

2004-07-23

We report exact model calculations of the spin-dependent tunneling in double magnetic tunnel junctions in the presence of impurities in the well. We show that the impurity can tune selectively the spin channels giving rise to a wide variety of interesting and novel transport phenomena. The tunneling magnetoresistance, the spin polarization, and the local current can be dramatically enhanced or suppressed by impurities. The underlying mechanism is the impurity-induced shift of the quantum well states (QWSs), which depends on the impurity potential, impurity position, and the symmetry of the QWS. Copyright 2004 The American Physical Society

Nucleic acid reactivity : challenges for next-generation semiempirical quantum models

PubMed Central

Huang, Ming; Giese, Timothy J.; York, Darrin M.

2016-01-01

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity in order to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic diffierential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models are evaluated against high-level quantum mechanical benchmark calculations for seven biologically important data sets. The data sets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling “modified divide-and-conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles within the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggest that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbond interactions. PMID:25943338

Theoretical investigations on molecular structure, vibrational spectra, HOMO, LUMO, NBO analysis and hyperpolarizability calculations of thiophene-2-carbohydrazide.

PubMed

Balachandran, V; Janaki, A; Nataraj, A

2014-01-24

The Fourier-Transform infrared and Fourier-Transform Raman spectra of thiophene-2-carbohydrazide (TCH) was recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1). Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of TCH were carried out by DFT (B3LYP) method with 6-311++G(d,p) as basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Stability of the molecule arising from hyper conjugative interaction and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecule have also been constructed. Copyright © 2013 Elsevier B.V. All rights reserved.

Renormalization of myoglobin–ligand binding energetics by quantum many-body effects

PubMed Central

Weber, Cédric; Cole, Daniel J.; O’Regan, David D.; Payne, Mike C.

2014-01-01

We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory. This combination of methods explicitly accounts for dynamical and multireference quantum physics, such as valence and spin fluctuations, of the 3d electrons, while treating a significant proportion of the protein (more than 1,000 atoms) with DFT. The computed electronic structure of the myoglobin complexes and the nature of the Fe–O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long-standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of the many-body effects induced by the Hund’s coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin. PMID:24717844

Quantum Mechanical Study of Nanoscale MOSFET

NASA Technical Reports Server (NTRS)

Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan

2001-01-01

The steady state characteristics of MOSFETS that are of practical Interest are the drive current, off-current, dope of drain current versus drain voltage, and threshold voltage. In this section, we show that quantum mechanical simulations yield significantly different results from drift-diffusion based methods. These differences arise because of the following quantum mechanical features: (I) polysilicon gate depletion in a manner opposite to the classical case (II) dependence of the resonant levels in the channel on the gate voltage, (III) tunneling of charge across the gate oxide and from source to drain, (IV) quasi-ballistic flow of electrons. Conclusions dI/dV versus V does not increase in a manner commensurate with the increase in number of subbands. - The increase in dI/dV with bias is much smaller then the increase in the number of subbands - a consequence of bragg reflection. Our calculations show an increase in transmission with length of contact, as seen in experiments. It is desirable for molecular electronics applications to have a small contact area, yet large coupling. In this case, the circumferential dependence of the nanotube wave function dictates: - Transmission in armchair tubes saturates around unity - Transmission in zigzag tubes saturates at two.

Single molecule quantum-confined Stark effect measurements of semiconductor nanoparticles at room temperature

NASA Astrophysics Data System (ADS)

Park, Kyoung Won; Deutsch, Zvicka; Li, J. Jack; Oron, Dan; Weiss, Shimon

2013-02-01

We investigate the quantum confined Stark effect (QCSE) of various nanoparticles (NPs) on the single molecule level at room temperature. We tested 8 different NPs with different geometry, material composition and electronic structure, and measured their QCSE by single molecule spectroscopy. This study reveals that suppressing the Coulomb interaction force between electron and hole by asymmetric type-II interface is critical for an enhanced QCSE. For example, ZnSe-CdS and CdSe(Te)-CdS-CdZnSe asymmetric nanorods (type-II) display respectively twice and more than three times larger QCSE than that of simple type-I nanorods (CdSe). In addition, wavelength blue-shift of QCSE and roughly linear Δλ-F (emission wavelength shift vs. the applied electric field) relation are observed for the type-II nanorods. Experimental results (Δλ-F or ΔE-F) are successfully reproduced by self-consistent quantum mechanical calculation. Intensity reduction in blue-shifted spectrum is also accounted for. Both calculations and experiments suggest that the magnitude of the QCSE is predominantly determined by the degree of initial charge separation in these structures.

The pursuit of locality in quantum mechanics

NASA Astrophysics Data System (ADS)

Hodkin, Malcolm

The rampant success of quantum theory is the result of applications of the 'new' quantum mechanics of Schrodinger and Heisenberg (1926-7), the Feynman-Schwinger-Tomonaga Quantum Electro-dynamics (1946-51), the electro-weak theory of Salaam, Weinberg, and Glashow (1967-9), and Quantum Chromodynamics (1973-); in fact, this success of 'the' quantum theory has depended on a continuous stream of brilliant and quite disparate mathematical formulations. In this carefully concealed ferment there lie plenty of unresolved difficulties, simply because in churning out fabulously accurate calculational tools there has been no sensible explanation of all that is going on. It is even argued that such an understanding is nothing to do with physics. A long-standing and famous illustration of this is the paradoxical thought-experiment of Einstein, Podolsky and Rosen (1935). Fundamental to all quantum theories, and also their paradoxes, is the location of sub-microscopic objects; or, rather, that the specification of such a location is fraught with mathematical inconsistency. This project encompasses a detailed, critical survey of the tangled history of Position within quantum theories. The first step is to show that, contrary to appearances, canonical quantum mechanics has only a vague notion of locality. After analysing a number of previous attempts at a 'relativistic quantum mechanics', two lines of thought are considered in detail. The first is the work of Wan and students, which is shown to be no real improvement on the iisu.al 'nonrelativistic' theory. The second is based on an idea of Dirac's - using backwards-in-time light-cones as the hypersurface in space-time. There remain considerable difficulties in the way of producing a consistent scheme here. To keep things nicely stirred up, the author then proposes his own approach - an adaptation of Feynman's QED propagators. This new approach is distinguished from Feynman's since the propagator or Green's function is not obtained by Feynman's rule. The type of equation solved is also different: instead of an initial-value problem, a solution that obeys a time-symmetric causality criterion is found for an inhomogeneous partial differential equation with homogeneous boundary conditions. To make the consideration of locality more precise, some results of Fourier transform theory are presented in a form that is directly applicable. Somewhat away from the main thrust of the thesis, there is also an attempt to explain, the manner in which quantum effects disappear as the number of particles increases in such things as experimental realisations of the EPR and de Broglie thought experiments.

The mechanism for water exchange in [UO(2)(H(2)O)(5)](2+) and [UO(2)(oxalate)(2)(H(2)O)](2-), as studied by quantum chemical methods.

PubMed

Vallet, V; Wahlgren, U; Schimmelpfennig, B; Szabó, Z; Grenthe, I

2001-12-05

The mechanisms for the exchange of water between [UO(2)(H(2)O)(5)](2+), [UO(2)(oxalate)(2)(H(2)O)](2)(-)(,) and water solvent along dissociative (D), associative (A) and interchange (I) pathways have been investigated with quantum chemical methods. The choice of exchange mechanism is based on the computed activation energy and the geometry of the identified transition states and intermediates. These quantities were calculated both in the gas phase and with a polarizable continuum model for the solvent. There is a significant and predictable difference between the activation energy of the gas phase and solvent models: the energy barrier for the D-mechanism increases in the solvent as compared to the gas phase, while it decreases for the A- and I-mechanisms. The calculated activation energy, Delta U(++), for the water exchange in [UO(2)(H(2)O)(5)](2+) is 74, 19, and 21 kJ/mol, respectively, for the D-, A-, and I-mechanisms in the solvent, as compared to the experimental value Delta H(++) = 26 +/- 1 kJ/mol. This indicates that the D-mechanism for this system can be ruled out. The energy barrier between the intermediates and the transition states is small, indicating a lifetime for the intermediate approximately 10(-10) s, making it very difficult to distinguish between the A- and I-mechanisms experimentally. There is no direct experimental information on the rate and mechanism of water exchange in [UO(2)(oxalate)(2)(H(2)O)](2-) containing two bidentate oxalate ions. The activation energy and the geometry of transition states and intermediates along the D-, A-, and I-pathways were calculated both in the gas phase and in a water solvent model, using a single-point MP2 calculation with the gas phase geometry. The activation energy, Delta U(++), in the solvent for the D-, A-, and I-mechanisms is 56, 12, and 53 kJ/mol, respectively. This indicates that the water exchange follows an associative reaction mechanism. The geometry of the A- and I-transition states for both [UO(2)(H(2)O)(5)](2+) and [UO(2)(oxalate)(2)(H(2)O)](2-) indicates that the entering/leaving water molecules are located outside the plane formed by the spectator ligands.

A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments.

PubMed

Sellers, Benjamin D; James, Natalie C; Gobbi, Alberto

2017-06-26

Reducing internal strain energy in small molecules is critical for designing potent drugs. Quantum mechanical (QM) and molecular mechanical (MM) methods are often used to estimate these energies. In an effort to determine which methods offer an optimal balance in accuracy and performance, we have carried out torsion scan analyses on 62 fragments. We compared nine QM and four MM methods to reference energies calculated at a higher level of theory: CCSD(T)/CBS single point energies (coupled cluster with single, double, and perturbative triple excitations at the complete basis set limit) calculated on optimized geometries using MP2/6-311+G**. The results show that both the more recent MP2.X perturbation method as well as MP2/CBS perform quite well. In addition, combining a Hartree-Fock geometry optimization with a MP2/CBS single point energy calculation offers a fast and accurate compromise when dispersion is not a key energy component. Among MM methods, the OPLS3 force field accurately reproduces CCSD(T)/CBS torsion energies on more test cases than the MMFF94s or Amber12:EHT force fields, which struggle with aryl-amide and aryl-aryl torsions. Using experimental conformations from the Cambridge Structural Database, we highlight three example structures for which OPLS3 significantly overestimates the strain. The energies and conformations presented should enable scientists to estimate the expected error for the methods described and we hope will spur further research into QM and MM methods.

Quantum-mechanical calculations of magnesium aspartate arginine structure and spectroscopic characteristics

NASA Astrophysics Data System (ADS)

Marcoin, W.; Pasterny, K.; Wrzalik, R.

2005-05-01

Theoretical calculations of magnesium aspartate-arginine (Mg[Asp-Arg]) structure and spectroscopic characteristics have been performed in the gas phase with the GAUSSIAN 98 software package using density functional theory (DFT) at the B3PW91 level. The 6-31+G* basis set was selected due to their reasonable quality and size. The comparison with corresponding results for magnesium aspartate-glycine (Mg[Asp-Gly]) is presented. NMR and IR measurements were carried out and obtained experimental 1H and 13C chemical shifts and IR spectra are compared with calculated spectral parameters.

Nucleon matter equation of state, particle number fluctuations, and shear viscosity within UrQMD box calculations

NASA Astrophysics Data System (ADS)

Motornenko, A.; Bravina, L.; Gorenstein, M. I.; Magner, A. G.; Zabrodin, E.

2018-03-01

Properties of equilibrated nucleon system are studied within the ultra-relativistic quantum molecular dynamics (UrQMD) transport model. The UrQMD calculations are done within a finite box with periodic boundary conditions. The system achieves thermal equilibrium due to nucleon-nucleon elastic scattering. For the UrQMD-equilibrium state, nucleon energy spectra, equation of state, particle number fluctuations, and shear viscosity η are calculated. The UrQMD results are compared with both, statistical mechanics and Chapman-Enskog kinetic theory, for a classical system of nucleons with hard-core repulsion.

Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Roonasi, Payman; Assle taghipour, Khatoon; van der Spoel, David; Manzetti, Sergio

2015-07-01

The quantum chemical calculations at the DFT/B3LYP level of theory were carried out on seven quinoxaline compounds, which have been synthesized as anti-Mycobacterium tuberculosis agents. Three conformers were optimized for each compound and the lowest energy structure was found and used in further calculations. The electronic properties including EHOMO, ELUMO and related parameters as well as electron density around oxygen and nitrogen atoms were calculated for each compound. The relationship between the calculated electronic parameters and biological activity of the studied compounds were investigated. Six similar quinoxaline derivatives with possible more drug activity were suggested based on the calculated electronic descriptors. A mechanism was proposed and discussed based on the calculated electronic parameters and bond dissociation energies.

Mixed Quantum/Classical Theory for Molecule-Molecule Inelastic Scattering: Derivations of Equations and Application to N2 + H2 System.

PubMed

Semenov, Alexander; Babikov, Dmitri

2015-12-17

The mixed quantum classical theory, MQCT, for inelastic scattering of two molecules is developed, in which the internal (rotational, vibrational) motion of both collision partners is treated with quantum mechanics, and the molecule-molecule scattering (translational motion) is described by classical trajectories. The resultant MQCT formalism includes a system of coupled differential equations for quantum probability amplitudes, and the classical equations of motion in the mean-field potential. Numerical tests of this theory are carried out for several most important rotational state-to-state transitions in the N2 + H2 system, in a broad range of collision energies. Besides scattering resonances (at low collision energies) excellent agreement with full-quantum results is obtained, including the excitation thresholds, the maxima of cross sections, and even some smaller features, such as slight oscillations of energy dependencies. Most importantly, at higher energies the results of MQCT are nearly identical to the full quantum results, which makes this approach a good alternative to the full-quantum calculations that become computationally expensive at higher collision energies and for heavier collision partners. Extensions of this theory to include vibrational transitions or general asymmetric-top rotor (polyatomic) molecules are relatively straightforward.

Raman bandshape analysis on CH and CSC stretching modes of dimethyl sulfoxide in liquid binary mixture: comparative study with quantum-chemical calculations.

PubMed

Upadhyay, Ganesh; Gomti Devi, Th

2014-12-10

The interacting nature of dimethyl sulfoxide (DMSO) in binary mixtures has been carried out on CH and CSC stretching modes of vibration using chloroform (CLF), chloroform-d (CLFd), acetonitrile (ACN) and acetonitrile-d3 (ACNd) solvents. Peak frequencies of both the stretching modes show blue shift with the increase in solvent concentration. Variation of Raman bandwidth with the solvent concentration was discussed using different mechanisms. Ab initio calculation for geometry optimization and vibrational wavenumber calculation have been performed on monomer and dimer structures of DMSO to explain the experimentally observed Raman spectra. Theoretically calculated values are found in good agreement with the experimental results. Vibrational and reorientational relaxation times have been studied corresponding to solvent concentrations to elucidate the interacting mechanisms of binary mixtures. Copyright © 2014 Elsevier B.V. All rights reserved.

From Waves to Particle Tracks and Quantum Probabilities

NASA Astrophysics Data System (ADS)

Falkenburg, Brigitte

Here, the measurement methods for identifying massive charged particles are investigated. They have been used from early cosmic ray studies up to the present day. Laws such as the classical Lorentz force and Einstein's relativistic kinematics were established before the rise of quantum mechanics. Later, it became crucial to measure the energy loss of charged particles in matter. In 1930, Bethe developed a semi-classical model based on the quantum mechanics of scattering. In the early 1930s, he and others calculated the passage of charged particles through matter including pair creation and bremsstrahlung. Due to missing trust in quantum electrodynamics, however, only semi-empirical methods were employed in order to estimate the mass and charge from the features of particle tracks. In 1932, Anderson inserted a lead plate into the cloud chamber in order to determine the flight direction and charge of the `positive electron'. In the 1940s, nuclear emulsions helped to resolve puzzles about particle identification and quantum electrodynamics. Later, the measurement theory was extended in a cumulative process by adding conservation laws for dynamic properties, probabilistic quantum formulas for resonances, scattering cross sections, etc. The measurement method was taken over from cosmic ray studies to the era of particle accelerators, and finally taken back from there to astroparticle physics. The measurement methods remained the same, but in the transition from particle to astroparticle physics the focus of interest shifted. Indeed, the experimental methods of both fields explore the grounds of `new physics' in complementary ways.

Simulations of defect spin qubits in piezoelectric semiconductors

NASA Astrophysics Data System (ADS)

Seo, Hosung

In recent years, remarkable advances have been reported in the development of defect spin qubits in semiconductors for solid-state quantum information science and quantum metrology. Promising spin qubits include the nitrogen-vacancy center in diamond, dopants in silicon, and the silicon vacancy and divacancy spins in silicon carbide. In this talk, I will highlight some of our recent efforts devoted to defect spin qubits in piezoelectric wide-gap semiconductors for potential applications in mechanical hybrid quantum systems. In particular, I will describe our recent combined theoretical and experimental study on remarkably robust quantum coherence found in the divancancy qubits in silicon carbide. We used a quantum bath model combined with a cluster expansion method to identify the microscopic mechanisms behind the unusually long coherence times of the divacancy spins in SiC. Our study indicates that developing spin qubits in complex crystals with multiple types of atom is a promising route to realize strongly coherent hybrid quantum systems. I will also discuss progress and challenges in computational design of new spin defects for use as qubits in piezoelectric crystals such as AlN and SiC, including a new defect design concept using large metal ion - vacancy complexes. Our first principles calculations include DFT computations using recently developed self-consistent hybrid density functional theory and large-scale many-body GW theory. This work was supported by the National Science Foundation (NSF) through the University of Chicago MRSEC under Award Number DMR-1420709.

Computational Materials Research

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A. (Editor); Gates, Thomas S. (Editor)

1996-01-01

Computational Materials aims to model and predict thermodynamic, mechanical, and transport properties of polymer matrix composites. This workshop, the second coordinated by NASA Langley, reports progress in measurements and modeling at a number of length scales: atomic, molecular, nano, and continuum. Assembled here are presentations on quantum calculations for force field development, molecular mechanics of interfaces, molecular weight effects on mechanical properties, molecular dynamics applied to poling of polymers for electrets, Monte Carlo simulation of aromatic thermoplastics, thermal pressure coefficients of liquids, ultrasonic elastic constants, group additivity predictions, bulk constitutive models, and viscoplasticity characterization.

Identification of Complex Carbon Nanotube Structures

NASA Technical Reports Server (NTRS)

Han, Jie; Saini, Subhash (Technical Monitor)

1998-01-01

A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

A direct evidence of vibrationally delocalized response at ice surface.

PubMed

Ishiyama, Tatsuya; Morita, Akihiro

2014-11-14

Surface-specific vibrational spectroscopic responses at isotope diluted ice and amorphous ice are investigated by molecular dynamics (MD) simulations combined with quantum mechanics/molecular mechanics calculations. The intense response specific to the ordinary crystal ice surface is predicted to be significantly suppressed in the isotopically diluted and amorphous ices, demonstrating the vibrational delocalization at the ordinary ice surface. The collective vibration at the ice surface is also analyzed with varying temperature by the MD simulation.

Nuclear quantum effects and kinetic isotope effects in enzyme reactions.

PubMed

Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas

2015-09-15

Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. Copyright © 2015 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xiaoyao; Hall, Randall W.; Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H{sub 2}O, N{sub 2}, and F{sub 2} molecules. The method is based on Feynman’s path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of othermore » quantum chemical methods and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.« less

Disappearing Q operator

NASA Astrophysics Data System (ADS)

Jones, H. F.; Rivers, R. J.

2007-01-01

In the Schrödinger formulation of non-Hermitian quantum theories a positive-definite metric operator η≡e-Q must be introduced in order to ensure their probabilistic interpretation. This operator also gives an equivalent Hermitian theory, by means of a similarity transformation. If, however, quantum mechanics is formulated in terms of functional integrals, we show that the Q operator makes only a subliminal appearance and is not needed for the calculation of expectation values. Instead, the relation to the Hermitian theory is encoded via the external source j(t). These points are illustrated and amplified for two non-Hermitian quantum theories: the Swanson model, a non-Hermitian transform of the simple harmonic oscillator, and the wrong-sign quartic oscillator, which has been shown to be equivalent to a conventional asymmetric quartic oscillator.

Disappearing Q operator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, H. F.; Rivers, R. J.

In the Schroedinger formulation of non-Hermitian quantum theories a positive-definite metric operator {eta}{identical_to}e{sup -Q} must be introduced in order to ensure their probabilistic interpretation. This operator also gives an equivalent Hermitian theory, by means of a similarity transformation. If, however, quantum mechanics is formulated in terms of functional integrals, we show that the Q operator makes only a subliminal appearance and is not needed for the calculation of expectation values. Instead, the relation to the Hermitian theory is encoded via the external source j(t). These points are illustrated and amplified for two non-Hermitian quantum theories: the Swanson model, a non-Hermitianmore » transform of the simple harmonic oscillator, and the wrong-sign quartic oscillator, which has been shown to be equivalent to a conventional asymmetric quartic oscillator.« less

Photoluminescence emission from GaAs nanodisks in GaAs/AlGaAs nanopillar arrays fabricated by neutral beam etching

NASA Astrophysics Data System (ADS)

Ohori, Daisuke; Fukuyama, Atsuhiko; Sakai, Kentaro; Higo, Akio; Thomas, Cedric; Samukawa, Seiji; Ikari, Tetsuo

2017-05-01

GaAs quantum nanodisks (QNDs) in nanopillar (NP) arrays are considered to be an attractive candidate for photonic device applications. We report a damageless fabrication technique that can be used to produce large-area lattice-matched GaAs/AlGaAs heterostructure NP arrays through the use of a bio-template and neutral beam etching. We have successfully realized GaAs QNDs in NPs owing to nanoscale iron oxide masks included in poly(ethylene glycol)-decorated ferritin protein shells. We observed for first time the photoluminescence emission from as-etched GaAs QNDs and confirmed quantum confinement by quantum mechanical calculation. Our methodology is vital for high-efficiency pillar-based optoelectronic devices such as NP laser diodes.

Quantum Time Evolution in a Qubit Readout Process with a Josephson Bifurcation Amplifier

NASA Astrophysics Data System (ADS)

Nakano, Hayato; Saito, Shiro; Semba, Kouichi; Takayanagi, Hideaki

2009-06-01

We analyzed the Josephson bifurcation amplifier (JBA) readout process of a superconducting qubit quantum mechanically by calculating the dynamics of the density operator of a driven nonlinear oscillator and a qubit coupled system during the measurement process. In purely quantum cases, bifurcation is impossible. Introducing decoherence enables us to reproduce the bifurcation with a finite hysteresis. When a qubit is initially in a superposition state, we have observed the qubit-probe (JBA) entangled state, and it is divided into two separable states at the moment the JBA transition begins. This corresponds to “projection.” To readout the measurement result, however, we must wait until the two JBA states are macroscopically well separated. The waiting time is determined by the strength of the decoherence in the JBA.

Applications of Quantum Theory of Atomic and Molecular Scattering to Problems in Hypersonic Flow

NASA Technical Reports Server (NTRS)

Malik, F. Bary

1995-01-01

The general status of a grant to investigate the applications of quantum theory in atomic and molecular scattering problems in hypersonic flow is summarized. Abstracts of five articles and eleven full-length articles published or submitted for publication are included as attachments. The following topics are addressed in these articles: fragmentation of heavy ions (HZE particles); parameterization of absorption cross sections; light ion transport; emission of light fragments as an indicator of equilibrated populations; quantum mechanical, optical model methods for calculating cross sections for particle fragmentation by hydrogen; evaluation of NUCFRG2, the semi-empirical nuclear fragmentation database; investigation of the single- and double-ionization of He by proton and anti-proton collisions; Bose-Einstein condensation of nuclei; and a liquid drop model in HZE particle fragmentation by hydrogen.