Quantum chemical calculations of glycine glutaric acid
Arioǧlu, ćaǧla; Tamer, Ömer; Avci, Davut; Atalay, Yusuf
2017-02-01
Density functional theory (DFT) calculations of glycine glutaric acid were performed by using B3LYP levels with 6-311++G(d,p) basis set. The theoretical structural parameters such as bond lengths and bond angles are in a good agreement with the experimental values of the title compound. HOMO and LUMO energies were calculated, and the obtained energy gap shows that charge transfer occurs in the title compound. Vibrational frequencies were calculated and compare with experimental ones. 3D molecular surfaces of the title compound were simulated using the same level and basis set. Finally, the 13C and 1H NMR chemical shift values were calculated by the application of the gauge independent atomic orbital (GIAO) method.
Reactivity of Tourmaline by Quantum Chemical Calculations
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
ZnAb initio calculations on reactivity of tourmaline were performed using both Gaussian and density function theory discrete variation method (DFT-DVM). The HF, B3LYP methods and basis sets STO-3G(3d,3p),6-31G(3d,3p) and 6-311++G(3df,3pd) were used in the calculations. The experimental results show energy value obtained from B3LYP and 6-31++1G(3df,3pd) basis sets is more accurate than those from other methods. The highest occupied molecular orbital (HOMO) of the tourmaline cluster mainly consists of O atom of hydroxyl group with relative higher energy level, suggesting that chemical bond between those of electron acceptor and this site may readily form, indicating the higher reactivity of hydroxyl group. The lowest unoccupied molecular orbital (LUMO) of the tourmaline cluster are dominantly composed of Si, O of tetrahedron and Na with relative lower energy level, suggesting that these atoms may tend to form chemical bond with those of electron donor. The results also prove that the O atoms of the tourmaline cluster have stronger reactivity than other atoms.
Quantum-chemical calculations of dye-sensitized semiconductor nanocrystals
Persson, P.; Lundqvist, M. J.; Nilsing, M.; van Duin, A. C. T.; Goddard, W. A., III
2006-08-01
Quantum chemical calculations providing detailed information of dye-sensitized semiconductor nanocrystals are presented. The calculations are used to elucidate both structural and electronic properties of photoelectrochemical devices, such as environmentally friendly Dye-Sensitized Solar Cells (DSSCs), at the molecular level. Quantum chemical calculations have recently been performed on both organic and organometallic dye molecules attached to titanium dioxide (TiO II) nanocrystals via different anchor and spacer groups. Strategies to make accurate quantum chemical calculations, e.g. at the DFT level of theory, on increasingly realistic models of such dye-sensitized semiconductor interfaces are presented. The ability of different anchor and spacer groups to act as mediators of ultrafast photo-induced electron injection from the dye molecules into the semiconductor nanocrystals is, in particular, discussed in terms of calculated electronic coupling strengths, and direct comparisons with experimental information are made whenever possible. Progress in the development of multi-scale simulation techniques using so called reactive force fields is illustrated for dye-sensitized solar cell systems.
Spectroscopic and quantum chemical calculation study on 2-ethoxythiazole molecule
Avcı, Davut; Dede, Bülent; Bahçeli, Semiha; Varkal, Döndü
2017-06-01
In this study, the 2-ethoxythiazole molecule (C5H7NSO) which is a member of the five-membered heterocyles with one nitrogen atom group has been investigated by using the experimental UV-vis (in three different solvents) and FT-IR spectral results as well as some magnetic properties. Furthermore, the calculated molecular geometric parameters, vibrational wavenumbers, HOMO-LUMO energies, 1H and 13C NMR chemical shift values and natural bond orbitals (NBO) of the title molecule have been calculated at the B3LYP and HSEH1PBE levels of theory with the 6-311++G(d,p) basis set. The spectral results obtained from the quantum chemical calculations are in good agreement with the experimental results.
Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine
Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing
2016-12-01
Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.
Vibrational spectroscopic studies of Isoleucine by quantum chemical calculations.
Moorthi, P P; Gunasekaran, S; Ramkumaar, G R
2014-04-24
In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of Isoleucine (2-Amino-3-methylpentanoic acid). The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments, thermodynamics properties, NBO analyses, NMR chemical shifts and ultraviolet-visible spectral interpretation of Isoleucine have been studied by performing MP2 and DFT/cc-pVDZ level of theory. The FTIR, FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The UV-visible absorption spectra of the compound were recorded in the range of 200-800 nm. Computational calculations at MP2 and B3LYP level with basis set of cc-pVDZ is employed in complete assignments of Isoleucine molecule on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA-4 program. The calculated wavenumbers are compared with the experimental values. The difference between the observed and calculated wavenumber values of most of the fundamentals is very small. (13)C and (1)H nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method and compared with experimental results. The formation of hydrogen bond was investigated in terms of the charge density by the NBO calculations. Based on the UV spectra and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. Besides, molecular electrostatic potential (MEP) were investigated using theoretical calculations.
Frka, Sanja; Šala, Martin; Kroflič, Ana; Huš, Matej; Čusak, Alen; Grgić, Irena
2016-06-01
Methylnitrocatechols (MNCs) are secondary organic aerosol (SOA) tracers and major contributors to atmospheric brown carbon; however, their formation and aging processes in atmospheric waters are unknown. To investigate the importance of aqueous-phase electrophilic substitution of 3-methylcatechol with nitronium ion (NO2(+)), we performed quantum calculations of their favorable pathways. The calculations predicted the formation of 3-methyl-5-nitrocatechol (3M5NC), 3-methyl-4-nitrocatechol (3M4NC), and a negligible amount of 3-methyl-6-nitrocatechol (3M6NC). MNCs in atmospheric PM2 samples were further inspected by LC/(-)ESI-MS/MS using commercial as well as de novo synthesized authentic standards. We detected 3M5NC and, for the first time, 3M4NC. In contrast to previous reports, 3M6NC was not observed. Agreement between calculated and observed 3M5NC/3M4NC ratios cannot unambiguously confirm the electrophilic mechanism as the exclusive formation pathway of MNCs in aerosol water. However, the examined nitration by NO2(+) is supported by (1) the absence of 3M6NC in the ambient aerosols analyzed and (2) the constant 3M5NC/3M4NC ratio in field aerosol samples, which indicates their common formation pathway. The magnitude of error one could make by incorrectly identifying 3M4NC as 3M6NC in ambient aerosols was also assessed, suggesting the importance of evaluating the literature regarding MNCs with special care.
Tantillo, Dean J
2013-08-01
This Highlight describes applications of quantum chemical calculations to problems in natural products chemistry, including the elucidation of natural product structures (distinguishing between constitutional isomers, distinguishing between diastereomers, and assigning absolute configuration) and determination of reasonable mechanisms for their formation.
Quantum chemical calculations for polymers and organic compounds
Lopez, J.; Yang, C.
1982-01-01
The relativistic effects of the orbiting electrons on a model compound were calculated. The computational method used was based on 'Modified Neglect of Differential Overlap' (MNDO). The compound tetracyanoplatinate was used since empirical measurement and calculations along "classical" lines had yielded many known properties. The purpose was to show that for large molecules relativity effects could not be ignored and that these effects could be calculated and yield data in closer agreement to empirical measurements. Both the energy band structure and molecular orbitals are depicted.
Vibration spectroscopic analysis and quantum chemical calculation of thymine
Directory of Open Access Journals (Sweden)
FU Yichen
2014-02-01
Full Text Available In this paper,Raman and IR spectra of thymine(Th were measured respectively in this paper.Molecular structure of Th was optimized and it’s Raman and IR bands were calculated using B3LYP/6-311G(contain Density functional theory,DFT method.It was found that the calculated values match well with the experimental ones.The vibratinal frequencies of Th molecules were completely assigned with the assistance of Gauss View visualization software.
Liu, Jinfeng; Zhang, John Z H; He, Xiao
2016-01-21
Geometry optimization and vibrational spectra (infrared and Raman spectra) calculations of proteins are carried out by a quantum chemical approach using the EE-GMFCC (electrostatically embedded generalized molecular fractionation with conjugate caps) method (J. Phys. Chem. A, 2013, 117, 7149). The first and second derivatives of the EE-GMFCC energy are derived and employed in geometry optimization and vibrational frequency calculations for several test systems, including a polypeptide ((GLY)6), an α-helix (AKA), a β-sheet (Trpzip2) and ubiquitin (76 residues with 1231 atoms). Comparison of the present results with those obtained from full system QM (quantum mechanical) calculations shows that the EE-GMFCC approach can give accurate molecular geometries, vibrational frequencies and vibrational intensities. The EE-GMFCC method is also employed to simulate the amide I vibration of proteins, which has been widely used for the analysis of peptide and protein structures, and the results are in good agreement with the experimental observations.
FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations
Steinmann, Casper; Hansen, Anne S; Jensen, Jan H
2012-01-01
Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available for support, setup and lower the barrier of entry for usage by non-experts. We present a fragmentation methodology and accompanying tools called FragIt to help setup these calculations. It uses the SMARTS language to find chemically appropriate substructures in structures and is used to prepare input files for the fragment molecular orbital method in the GAMESS program package. We present patterns of fragmentation for proteins and polysaccharides, specifically D-galactopyranose for use in cyclodextrins.
Energy Technology Data Exchange (ETDEWEB)
Avakyan, V.G.; Volkova, V.V.; Gusel' nikov, L.E.; Ziegler, U.; Zimmermann, G.; Ondurshka, B.; Nametkin, N.S.
1987-04-01
In the study of the role of allyl type radicals in the pyrolysis of hydrocarbons it is of interest to investigate the conditions of formation, structure, and reactivity of 2-methylallyl radical (C/sub 4/H/sub 7//sup ./). The authors performed theoretical assignment of the bands, which were observed in the lattice spectra of the pyrolysis products, to the vibrations of the C/sub 4/H/sub 7//sup ./ radical by means of calculation of the frequencies and shapes of the normal vibrations. Since the necessary geometrical parameters and force coefficients of C/sub 4/H/sub 7//sup ./ are not known, they determined them by means of nonempirical quantum chemical calculation. The quantum chemical calculation of C/sub 4/H/sub 7//sup ./ was performed by means of the unrestricted Hartree-Fock method using STO-4G (geometry optimization taking into account the characteristics of calculation of radicals in minimal bases and calculation of the force coefficients by means of numerical differentiation) and 4-31G bases (electron density distribution) by means of GAUSSIAN-70 program. For comparison of the energy and electron density distribution they performed calculations also for the 2-methylallyl cation C/sub 4/H/sub 7//sup ./. From the calculation of the difference of the total energies of C/sub 4/H/sub 7//sup ./ and C/sub 4/H/sub 7//sup ./ in the 4-31G basis was 7.4 eV, which is comparable to the ionization energy of the 2-methylallyl radical, 7.95 eV.
Energy Technology Data Exchange (ETDEWEB)
Fayet, Guillaume [Laboratoire d' Electrochimie et Chimie Analytique, CNRS UMR-7575, Ecole Nationale Superieure de Chimie de Paris, 11 rue P. et M. Curie, 75231 Paris Cedex 05 (France); Institut National de l' Environnement Industriel et des Risques (INERIS), Parc Technologique Alata, BP2, 60550 Verneuil-en-Halatte (France); Rotureau, Patricia, E-mail: patricia.rotureau@ineris.fr [Institut National de l' Environnement Industriel et des Risques (INERIS), Parc Technologique Alata, BP2, 60550 Verneuil-en-Halatte (France); Joubert, Laurent; Adamo, Carlo [Laboratoire d' Electrochimie et Chimie Analytique, CNRS UMR-7575, Ecole Nationale Superieure de Chimie de Paris, 11 rue P. et M. Curie, 75231 Paris Cedex 05 (France)
2009-11-15
This work presents a new approach to predict thermal stability of nitroaromatic compounds based on quantum chemical calculations and on quantitative structure-property relationship (QSPR) methods. The data set consists of 22 nitroaromatic compounds of known decomposition enthalpy (taken as a macroscopic property related to explosibility) obtained from differential scanning calorimetry. Geometric, electronic and energetic descriptors have been selected and computed using density functional theory (DFT) calculation to describe the 22 molecules. First approach consisted in looking at their linear correlations with the experimental decomposition enthalpy. Molecular weight, electrophilicity index, electron affinity and oxygen balance appeared as the most correlated descriptors (respectively R{sup 2} = 0.76, 0.75, 0.71 and 0.64). Then multilinear regression was computed with these descriptors. The obtained model is a six-parameter equation containing descriptors all issued from quantum chemical calculations. The prediction is satisfactory with a correlation coefficient R{sup 2} of 0.91 and a predictivity coefficient R{sub cv}{sup 2} of 0.84 using a cross validation method.
Wu, Xin; Koslowski, Axel; Thiel, Walter
2012-07-10
In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.
Complementing high-throughput X-ray powder diffraction data with quantum-chemical calculations
DEFF Research Database (Denmark)
Naelapaa, Kaisa; van de Streek, Jacco; Rantanen, Jukka
2012-01-01
High-throughput crystallisation and characterisation platforms provide an efficient means to carry out solid-form screening during the pre-formulation phase. To determine the crystal structures of identified new solid phases, however, usually requires independent crystallisation trials to produce...... single crystals or bulk samples of sufficient quantity to carry out high-quality X-ray diffraction measurements. This process could be made more efficient by a robust procedure for crystal structure determination directly from high-throughput X-ray powder diffraction (XRPD) data. Quantum......-chemical calculations based on dispersion-corrected density functional theory (DFT-D) have now become feasible for typical small organic molecules used as active pharmaceutical ingredients. We demonstrate how these calculations can be applied to complement high-throughput XRPD data by determining the crystal structure...
Romańczyk, Piotr P; Rotko, Grzegorz; Kurek, Stefan S
2016-08-10
Formal potentials of the first reduction leading to dechlorination in dimethylformamide were obtained from convolution analysis of voltammetric data and confirmed by quantum chemical calculations for a series of polychlorinated benzenes: hexachlorobenzene (-2.02 V vs. Fc(+)/Fc), pentachloroanisole (-2.14 V), and 2,4-dichlorophenoxy- and 2,4,5-trichlorophenoxyacetic acids (-2.35 V and -2.34 V, respectively). The key parameters required to calculate the reduction potential, electron affinity and/or C-Cl bond dissociation energy, were computed at both DFT-D and CCSD(T)-F12 levels. Comparison of the obtained gas-phase energies and redox potentials with experiment enabled us to verify the relative energetics and the performance of various implicit solvent models. Good agreement with the experiment was achieved for redox potentials computed at the DFT-D level, but only for the stepwise mechanism owing to the error compensation. For the concerted electron transfer/C-Cl bond cleavage process, the application of a high level coupled cluster method is required. Quantum chemical calculations have also demonstrated the significant role of the π*ring and σ*C-Cl orbital mixing. It brings about the stabilisation of the non-planar, C2v-symmetric C6Cl6˙(-) radical anion, explains the experimentally observed low energy barrier and the transfer coefficient close to 0.5 for C6Cl5OCH3 in an electron transfer process followed by immediate C-Cl bond cleavage in solution, and an increase in the probability of dechlorination of di- and trichlorophenoxyacetic acids due to substantial population of the vibrational excited states corresponding to the out-of-plane C-Cl bending at ambient temperatures.
Vojta, Danijela; Dominković, Katarina; Miljanić, Snežana; Spanget-Larsen, Jens
2017-03-01
The molecular structures of myricetin (3,3‧,4‧,5,5‧,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR and Raman). In addition, a reassignment of the Cdbnd O stretching bands is suggested.
Institute of Scientific and Technical Information of China (English)
Ling-hong YU; Geng-tao LIU; You-min SUN; Hong-yu ZHANG
2004-01-01
AIM: To investigate the effect of schisanhenol (Sal) on copper ion-induced oxidative modulation of human low density lipoprotein (LDL). METHODS: The antioxidative activity of eight schisandrins (DCL) on microsome lipid peroxidation induced by Vit C/NADPH system was first observed, and then, the effect of Sal on Cu2+-induced human LDL oxidation was studied. The generation of malondialdehyde (MDA), lipofuscin, reactive oxygen species (ROS), consumption of α-tocopherol as well as electrophoretic mobility of LDL were determined as criteria of LDL oxidation. Finally, the quantum chemical method was used to calculate the theoretical parameters of eight DCL for elucidating the difference of their antioxidant ability. RESULTS: Sal was shown to be the most active one among eight schizandrins in inhibiting microsome lipid oxidation induced by Vit C/NADPH. Sal 100, 50, and 10 μrnol/L inhibited production of MDA, lipofuscin and ROS as well as the consumption of α-tocopherol in Cu2+-induced oxidation of human LDL in a dose-dependent manner. Sal also reduced electrophoretic mobility of the oxidized human LDL. Further study of quantum chemistry found that Sal was the strongest one among eight DCL to scavenge O-2, R·, RO·, and ROO· radicals. CONCLUSION: Sal has antioxidative effect on human LDL oxidation.The mechanism of Sal against LDL oxidation may be through scavenging free radicals.
Quantum chemical calculation of the equilibrium structures of small metal atom clusters
Kahn, L. R.
1982-01-01
Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.
Institute of Scientific and Technical Information of China (English)
Zeng Hui; Zhao Jun; Xiao Xun
2013-01-01
Quantum chemical calculations are performed to investigate the equilibrium C-COOH bond distances and the bond dissociation energies (BDEs) for 15 acids.These compounds are studied by utilizing the hybrid density functional theory (DFT) (B3LYP,B3PW91,B3P86,PBE1PBE) and the complete basis set (CBS-Q) method in conjunction with the 6-31 lG** basis as DFT methods have been found to have low basis sets sensitivity for small and medium molecules in our previous work.Comparisons between the computational results and the experimental values reveal that CBS-Q method,which can produce reasonable BDEs for some systems in our previous work,seems unable to predict accurate BDEs here.However,the B3P86 calculated results accord very well with the experimental values,within an average absolute error of 2.3 kcal/mol.Thus,B3P86 method is suitable for computing the reliable BDEs of C-COOH bond for carboxylic acid compounds.In addition,the energy gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of studied compounds are estimated,based on which the relative thermal stabilities of the studied acids are also discussed.
Sethi, Arun; Singh, Ranvijay Pratap; Prakash, Rohit; Amandeep
2017-02-01
In the present research paper corticosteroids prodrugs of hydrocortisone acetate (1) have been synthesized, which was isolated from the flowers of Allamanda Violacea. The hydrocortisone acetate (1) was hydrolyzed to hydrocortisone (2) which was subsequently converted to prednisolone (3). Both the hydrocortisone (1) and prednisolone (2) underwent Steglich esterification with naproxen and Ibuprofen yielding compounds 11, 17 dihydroxy-21-(2-(6-methoxynaphthalene-2yl) propionoxy)-pregn-4-ene-3, 20-dione (4), 11, 17-dihydroxy-21-(2-(4-isobutylphenyl) propionoxy)-pregn-4-ene-3, 20-dione (5), 21-(2-(6-methoxynaphthalene-2-yl) propionoxy) 11,17-di-hydroxy-3,20-diketo-pregn-1,4-diene (6) and 11,17-di-hydroxy-3,20-diketo-pregn-1,4-diene-21-yl-2-(4-isobutylphenyl) propanoate (7). The synthesized compounds have been characterized with the help of spectroscopic techniques like 1H, 13C NMR, FT-IR spectroscopy and mass spectrometry. Density functional theory (DFT) with B3LYP functional and 6-31G (d, p) basis set has been used for the Quantum chemical calculations. The electronic properties such as frontier orbitals and band gap energies were calculated by TD-DFT approach. Intramolecular interactions have been identified by AIM (Atoms in Molecule) approach and vibrational wavenumbers have been calculated using DFT method. The reactivity and reactive site within the synthesized prodrugs have been examined with the help of reactivity descriptors. Dipole moment, polarizability and first static hyperpolarizability have been calculated to get a better insight of the properties of synthesized prodrugs. The molecular electrostatic potential (MEP) surface analysis has also been carried out.
Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.
2014-05-01
The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.
Belyakov, Alexander V.; Nikolaenko, Kirill O.; Davidovich, Pavel B.; Ivanov, Anatolii D.; Garabadzhiu, Alexander V.; Rykov, Anatolii N.; Shishkov, Igor F.
2017-03-01
The molecular structure of isatin, indole-2,3-dione, was studied by gas-phase electron diffraction (GED) and quantum chemical calculations (M062X and MP2 methods with aug-cc-pVTZ basis set). The best fit of the experimental scattering intensities (R-factor = 4.4%) was obtained for a molecular model of Cs symmetry. The structure of the benzene ring deviates from a regular hexagon due to the adjacent pyrrole heterocycle. The small differences between similar geometric parameters were constrained at the values calculated at the M062X level. The experimental structural parameters agree well with the results of theoretical calculations. The bonds in the benzene moiety are in agreement with their standard values. The (Odbnd)Csbnd C(dbnd O) carbon-carbon bond of the pyrrole moiety (1.573(7) Å) is remarkably lengthened in comparison with standard C(sp2)sbnd C(sp2) value, 1.425(11) Å for N-methylpyrrole. According to NBO analysis of isatin, glyoxal and pyrrole-2,3-dione molecules this lengthening cannot be attributed to the steric interactions of Cdbnd O bonds alone and is, mainly, due to the electrostatic repulsion and hyperconjugation that is delocalization of oxygen lone pairs of π-type into the corresponding carbon-carbon antibonding orbital, nπ(O) → σ∗(Csbnd C). Deletion of σ∗(Csbnd C) orbital followed by subsequent geometry optimization led to shortening of the corresponding Csbnd C bond by 0.06 Å. According to different aromaticity descriptors, aromaticity of benzene moiety of isatin is smaller in comparison with benzene molecule. External magnetic field induces diatropic ring current in benzene moiety of isatin.
Musharraf, Syed Ghulam; Ul Arfeen, Qamar; Ul Haq, Faraz; Khatoon, Aliya; Azher Ali, Rahat
2017-06-26
Methyltestosterone is a synthetic testosterone derivative commonly used for the treatment of testosterone deficiency in males and one the anabolic steroids whose use is banned by World Anti-Doping Agency (WADA). This study presents a simple, cost-effective and rapid stability-indicating assay for densitometric quantification of methyltestosterone in pharmaceutical formulation. The developed method employed pre-coated TLC plates with mobile phase hexane:acetone (6.5:3.5 v/v). Limit of detection and limit of quantitation were found to be 2.06 and 6.24 ng/spot, respectively. Stress degradation study of methyltestosterone was conducted by applying various stress conditions such as hydrolysis under acidic, basic and neutral conditions, heating in anhydrous conditions and exposure to light. Methyltestosterone was found to be susceptible to photodegradation, acidic and basic hydrolysis. Degraded products were well resolved with significantly different Rf values. Acid degraded product was identified as 17,17-dimethyl-18-norandrosta-4,13(14)-dien-3-one through spectroscopic methods. The reactivity of methyltestosterone under applied stress conditions was also explained by quantum chemical calculations. The developed method is found to be repeatable, selective and accurate for quantification of methyltestosterone and can be employed for routine analysis. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Mariappan Balasekaran, Samundeeswari; Todorova, Tanya K; Pham, Chien Thang; Hartmann, Thomas; Abram, Ulrich; Sattelberger, Alfred P; Poineau, Frederic
2016-06-01
A simple method for the high-yield preparation of (NH4)2[Re2F8]·2H2O has been developed that involves the reaction of (n-Bu4N)2[Re2Cl8] with molten ammonium bifluoride (NH4HF2). Using this method, the new salt [NH4]2[Re2F8]·2H2O was prepared in ∼90% yield. The product was characterized in solution by ultraviolet-visible light (UV-vis) and (19)F nuclear magnetic resonance ((19)F NMR) spectroscopies and in the solid-state by elemental analysis, powder X-ray diffraction (XRD), and infrared (IR) spectroscopy. Multiconfigurational CASSCF/CASPT2 quantum chemical calculations were performed to investigate the molecular and electronic structure, as well as the electronic absorption spectrum of the [Re2F8](2-) anion. The metal-metal bonding in the Re2(6+) unit was quantified in terms of effective bond order (EBO) and compared to that of its [Re2Cl8](2-) and [Re2Br8](2-) analogues.
Enrique-Romero, J.; Rimola, A.; Ceccarelli, C.; Balucani, N.
2016-06-01
Complex Organic Molecules (COMs) have been detected in the interstellar medium (ISM). However, it is not clear whether their synthesis occurs on the icy surfaces of interstellar grains or via a series of gas-phase reactions. As a test case of the COMs synthesis in the ISM, we present new quantum chemical calculations on the formation of acetaldehyde (CH3CHO) from the coupling of the HCO and CH3 radicals, both in gas phase and on water ice surfaces. The binding energies of HCO and CH3 on the amorphous water ice were also computed (2333 and 734 K, respectively). Results indicate that, in gas phase, the products could be either CH3CHO, CH4 + CO, or CH3OCH, depending on the relative orientation of the two radicals. However, on the amorphous water ice, only the CH4 + CO product is possible due to the geometrical constraints imposed by the water ice surface. Therefore, acetaldehyde cannot be synthesized by the CH3 + HCO coupling on the icy grains. We discuss the implications of these results and other cases, such as ethylene glycol and dimethyl ether, in which similar situations can occur, suggesting that formation of these molecules on the grain surfaces might be unlikely.
Enrique-Romero, Joan; Ceccarelli, Cecilia; Balucani, Nadia
2016-01-01
Complex Organic Molecules (COMs) have been detected in the interstellar medium (ISM). However, it is not clear whether their synthesis occurs on the icy surfaces of interstellar grains or via a series of gas-phase reactions. As a test case of the COMs synthesis in the ISM, we present new quantum chemical calculations on the formation of acetaldehyde (CH3CHO) from the coupling of the HCO and CH3 radicals, both in gas phase and on water ice surfaces. The binding energies of HCO and CH3 on the amorphous water ice were also computed (2333 and 734 K, respectively). Results indicate that, in gas phase, the products could be either CH3CHO, CH4 + CO, or CH3OCH, depending on the relative orientation of the two radicals. However, on the amorphous water ice, only the CH4 + CO product is possible due to the geometrical constraints imposed by the water ice surface. Therefore, acetaldehyde cannot be synthesized by the CH3 + HCO coupling on the icy grains. We discuss the implications of these results and other cases, such a...
Gobinath, E; Xavier, R John
2013-03-01
The complete vibrational assignment and analysis of the fundamental modes of 2-bromo-5-nitrothiazole (BNT) was carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the ab initio HF and DFT-B3LYP gradient calculations employing 6-311++G(d,p) basis set. Thermodynamic properties like entropy, heat capacity and zero point energy 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 properties such as electric dipole moment and first hyperpolarizability of BNT have been computed using B3LYP quantum chemical calculation.
Busch, Anna; González-García, Núria; Lendvay, György; Olzmann, Matthias
2015-07-16
The thermal decomposition of cyanonitrene, NCN, was studied behind reflected shock waves in the temperature range 1790-2960 K at pressures near 1 and 4 bar. Highly diluted mixtures of NCN3 in argon were shock-heated to produce NCN, and concentration-time profiles of C atoms as reaction product were monitored with atomic resonance absorption spectroscopy at 156.1 nm. Calibration was performed with methane pyrolysis experiments. Rate coefficients for the reaction (3)NCN + M → (3)C + N2 + M (R1) were determined from the initial slopes of the C atom concentration-time profiles. Reaction R1 was found to be in the low-pressure regime at the conditions of the experiments. The temperature dependence of the bimolecular rate coefficient can be expressed with the following Arrhenius equation: k1(bim) = (4.2 ± 2.1) × 10(14) exp[-242.3 kJ mol(-1)/(RT)] cm(3) mol(-1) s(-1). The rate coefficients were analyzed by using a master equation with specific rate coefficients from RRKM theory. The necessary molecular data and energies were calculated with quantum chemical methods up to the CCSD(T)/CBS//CCSD/cc-pVTZ level of theory. From the topography of the potential energy surface, it follows that reaction R1 proceeds via isomerization of NCN to CNN and subsequent C-N bond fission along a collinear reaction coordinate without a tight transition state. The calculations reproduce the magnitude and temperature dependence of the rate coefficient and confirm that reaction R1 is in the low-pressure regime under our experimental conditions.
Ferres, Lynn; Stahl, Wolfgang; Nguyen, Ha Vinh Lam
2016-06-01
A pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2 - 26.5 GHz was used to measure the spectrum of phenetole (ethyl phenyl ether or ethoxybenzene, C6H5OC2H5). The conformational landscape is completely determined by the orientations of the phenyl ring and the ethyl group. A two-dimensional potential energy surface was calculated at the MP2/6-311++G(d,p) level of theory. Two conformers were found: The trans conformer has a Cs symmetry, and the gauche conformer has the ethyl group tilted out of the phenyl plane by about 70°. Totally 186 rotational transitions were assigned to the more stable planar trans conformer, and fitted using a semi-rigid rotor model to measurement accuracy of 2 kHz. Highly accurate rotational and centrifugal distortion constants were determined. Several method and basis set combinations were applied to check for convergence and to compare with the experimentally deduced molecular parameters. The inertial defect of the observed conformer Δc = (Ic - Ia - Ib) = -6.718 uÅ2 confirms that the heavy atom skeleton is planar with two pairs of hydrogen atoms out of plane. All lines in the spectrum could be assigned to the trans conformer, which confirms that the gauche conformer cannot be observed under our measurement conditions. In agreement with the rather high torsional barrier of the methyl group (V3 = 1168 wn) calculated by quantum chemical methods, all assigned lines appeared sharp and no signs of splittings were observed for the methyl internal rotation.
Energy Technology Data Exchange (ETDEWEB)
Mariappan Balasekaran, Samundeeswari; Todorova, Tanya K.; Pham, Chien Thang; Hartmann, Thomas; Abram, Ulrich; Sattelberger, Alfred P.; Poineau, Frederic
2016-06-06
A simple method for the high-yield preparation of (NH_{4})_{2}[Re_{2}F_{8}]· 2H_{2}O has been developed that involves the reaction of (n-Bu_{4}N)2[Re_{2}Cl_{8}] with molten ammonium bifluoride (NH_{4}HF_{2}). Using this method, the new salt [NH_{4}]_{2}[Re_{2}F_{8}]·2H_{2}O was prepared in ~90% yield. The product was characterized in solution by ultraviolet-visible light (UV-vis) and ^{19}F nuclear magnetic resonance (19F NMR) spectroscopies and in the solid-state by elemental analysis, powder X-ray diffraction (XRD), and infrared (IR) spectroscopy. Multiconfigurational CASSCF/CASPT2 quantum chemical calculations were performed to investigate the molecular and electronic structure, as well as the electronic absorption spectrum of the [Re_{2}F_{8}] ^{2-} anion. The metal-metal bonding in the Re_{2} ^{6+} unit was quantified in terms of effective bond order (EBO) and compared to that of its [Re_{2}Cl_{8}] ^{2-} and [Re_{2}Br_{8}] ^{2-} analogues.
Zhu, Junsheng; Liu, Anmin; Wang, Dianlong
2017-09-01
A general strategy is demonstrated to achieve superior lithium storage properties by constructing Sn/graphene nanocomposite architecture. The synergistic lithium storage performance of Sn/graphene is initially investigated by quantum chemical calculations based on density functional theory. Results show that the electronic conductivity of Sn/graphene is superior to that of Sn metal. Subsequently, a facile precipitation method is designed to fabricate Sn/graphene composites. SEM and TEM analysis reveals that Sn nanoparticles (40-80 nm) are homogenously sandwiched between graphene nanosheets. Cyclic voltammetry and galvanostatic charge/discharge measurements show that Sn/graphene composites exhibit superior lithium storage capability as compared to bare Sn. The enhanced performance is further investigated by electrochemical impedance spectroscopy. Results suggest that the addition of graphene in the nanocomposites significantly improves the electron transfer, which is consistent with the quantum chemical calculations.
Gonta, Svetlana; Utinans, Maris; Kirilov, Georgii; Belyakov, Sergey; Ivanova, Irena; Fleisher, Mendel; Savenkov, Valerij; Kirilova, Elena
2013-01-01
Several new substituted amidine derivatives of benzanthrone were synthesized by a condensation reaction from 3-aminobenzo[de]anthracen-7-one and appropriate aromatic and aliphatic amides. The obtained derivatives have a bright yellow or orange fluorescence in organic solvents and in solid state. The novel benzanthrone derivatives were characterized by TLC analysis, 1H NMR, IR, MS, UV/vis, and fluorescence spectroscopy. The solvent effect on photophysical behaviors of these dyes was investigated, and the results showed that the Stoke's shift increased, whereas quantum yield decreased with the growth of the solvent polarity. The structure of some dyes was confirmed by the X-ray single crystal structure analysis. AM1, ZINDO/S and ab initio calculations using Gaussian software were carried out to estimate the electron system of structures. The calculations show planar configurations for the aromatic core of these compounds and two possible orientations of amidine substituents. The calculation results correlate well with red-shifted absorption and emission spectra of compounds.
A general intermolecular force field based on tight-binding quantum chemical calculations
Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas
2017-10-01
A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.
Nagabalasubramanian, P B; Periandy, S; Karabacak, Mehmet; Govindarajan, M
2015-06-15
The solid phase FT-IR and FT-Raman spectra of 4-vinylcyclohexene (abbreviated as 4-VCH) have been recorded in the region 4000-100cm(-1). The optimized molecular geometry and vibrational frequencies of the fundamental modes of 4-VCH have been precisely assigned and analyzed with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method at 6-311++G(d,p) level basis set. The theoretical frequencies were properly scaled and compared with experimentally obtained FT-IR and FT-Raman spectra. Also, the effect due the substitution of vinyl group on the ring vibrational frequencies was analyzed and a detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated total energy distribution (TED). The time dependent DFT (TD-DFT) method was employed to predict its electronic properties, such as electronic transitions by UV-Visible analysis, HOMO and LUMO energies, molecular electrostatic potential (MEP) and various global reactivity and selectivity descriptors (chemical hardness, chemical potential, softness, electrophilicity index). Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Atomic charges obtained by Mulliken population analysis and NBO analysis are compared. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are also calculated.
Directory of Open Access Journals (Sweden)
Manoel A M Filho
Full Text Available The RM1 quantum chemical model for the calculation of complexes of Tm(III, Yb(III and Lu(III is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications.
Filho, Manoel A M; Dutra, José Diogo L; Rocha, Gerd B; Simas, Alfredo M; Freire, Ricardo O
2016-01-01
The RM1 quantum chemical model for the calculation of complexes of Tm(III), Yb(III) and Lu(III) is advanced. Subsequently, we tested the models by fully optimizing the geometries of 126 complexes. We then compared the optimized structures with known crystallographic ones from the Cambridge Structural Database. Results indicate that, for thulium complexes, the accuracy in terms of the distances between the lanthanide ion and its directly coordinated atoms is about 2%. Corresponding results for ytterbium and lutetium are both 3%, levels of accuracy useful for the design of lanthanide complexes, targeting their countless applications.
Delgado, Eduardo J; Alderete, Joel
2002-01-01
The Henry's law constants for all 12 polychlorinated benzene congeners were calculated using semiempirical quantum chemical solvation models (SM2, SM2.1, and SM3), and their performances are discussed. The values obtained by the SM3 method are underestimated compared with the experimental values and those calculated by SM2 and SM2.1 methods. This underestimation is larger as the degree of chlorination of the benzenes increases. This bad performance of SM3 to calculate Henry's law constants is attributable to the PM3 Hamiltonian, due to its incapacity to give a good description of electron density in chlorinated benzenes. The best results, within the 95% confidence limit of error of the experimental mean, are obtained using SM2 method. The discussion includes analysis of the different contributions to the free energy of solvation, namely, polarization free energy, cavitation, dispersion, and structural rearrangement of the solvent effects as well as partial atomic charges.
Ganesan, Aravindhan; Wang, Feng; Brunger, Michael; Prince, Kevin
2011-09-01
Effects of alkyl side chains (R-) on the electronic structural properties of aliphatic amino acids are investigated using quantum mechanical approaches. The carbon (C 1s) binding energy spectra of the aliphatic amino acids are derived from the C 1s spectrum of glycine (the parent spectrum) by the addition of spectral peaks, depending on the alkyl side chains, appearing in the lower energy region IP aliphatic amino acids owing to perturbations depending on the size and structure of the alkyl chains. The pattern of the N 1s and O 1s spectra in glycine is retained in the spectra of the other amino acids with small shifts to lower energy, again depending on the alkyl side chain. The Hirshfeld charge analyses confirm the observations. The alkyl effects on the valence binding energy spectra of the amino acids are concentrated in the middle valence energy region of 12-16 eV, and hence this energy region of 12-16 eV is considered as the `fingerprint' of the alkyl side chains. Selected valence orbitals, either inside or outside of the alkyl fingerprint region, are presented using both density distributions and orbital momentum distributions, in order to understand the chemical bonding of the amino acids. It is also observed that the HOMO-LUMO energy gaps of the aliphatic amino acids are reduced with the growth of the alkyl side chain.
Pimenov, Oleg A.; Belova, Natalya V.; Sliznev, Valery V.
2017-03-01
The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione thulium, or Tm(thd)3, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both the DFT(PBE0) calculations and the GED data collected at 400(8) K indicate that the molecules have D3 symmetry with a distorted antiprismatic TmO6 coordination geometry. According to GED refinements the twist angle θ, i.e. the angle of rotation of the upper O3 triangles relative to their position in regular prism is θ = 16.9(2.0)0. This value is close to both the equilibrium value obtained from the DFT calculations and to the thermal average value at the temperature of the GED experiment obtained by integration over the DFT potential energy surface. The bond distances (rh1) in the chelate ring are Tmsbnd O = 2.214(5) Å, Csbnd O = 1.278(4) Å, and Csbnd C = 1.404(3) Å. The DFT calculations yielded structure parameters in close agreement with those found experimentally. As an alternative to conventional Lewis model which was realized in NBO the topological analysis of ρ(r) in the frame of Bader's quantum theory of atoms in molecule (QTAIM) was performed.
Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K; Chibotaru, Liviu F; Delcey, Mickaël G; De Vico, Luca; Fdez Galván, Ignacio; Ferré, Nicolas; Frutos, Luis Manuel; Gagliardi, Laura; Garavelli, Marco; Giussani, Angelo; Hoyer, Chad E; Li Manni, Giovanni; Lischka, Hans; Ma, Dongxia; Malmqvist, Per Åke; Müller, Thomas; Nenov, Artur; Olivucci, Massimo; Pedersen, Thomas Bondo; Peng, Daoling; Plasser, Felix; Pritchard, Ben; Reiher, Markus; Rivalta, Ivan; Schapiro, Igor; Segarra-Martí, Javier; Stenrup, Michael; Truhlar, Donald G; Ungur, Liviu; Valentini, Alessio; Vancoillie, Steven; Veryazov, Valera; Vysotskiy, Victor P; Weingart, Oliver; Zapata, Felipe; Lindh, Roland
2016-02-15
In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. © 2015 Wiley Periodicals, Inc.
Directory of Open Access Journals (Sweden)
Ahmed A. El-Henawy
2013-04-01
Full Text Available Anti-leukemia screening of previously prepared isothiouronium and quaternary salts was performed, and some salts exhibited promising activity as anticancer agents. Quantum chemical calculations were utilized to explore the electronic structure and stability of these compounds. Computational studies have been carried out at the PM3 semiempirical molecular orbitals level, to establish the HOMO-LUMO, IP and ESP mapping of these compounds. The ADMET properties were also studied to gain a clear view of the potential oral bioavailability of these compounds. The surface properties calculated included critical micelle concentration (CMC, maximum surface excess (Γmax, minimum surface area (Amin, free energy of micellization (ΔGomic and adsorption (ΔGoads.
Bytheway, Ian; Darley, Michael G; Popelier, Paul L A
2008-03-01
The calculation of polar surface areas (PSA) from the electron density using quantum chemical topology (QCT) and a newly developed algorithm to determine isodensity surface areas is described. PSA values were calculated from the atomic partitioning of B3LYP/6-311G* wavefunctions and the results described herein represent the first application of this new algorithm. PSA values were calculated for forty drugs and compared to the topological polar surface area (TPSA) and those calculated by the QikProp program. Oral bioavailabilities predicted from the QCT PSA values for a subset of twenty drugs (the Palm set) were similar to those predicted by the dynamic polar surface area (DPSA) and in general, are in agreement with the observed values. Overall, PSA values obtained from QCT were generally similar to the DPSA, TPSA, and QikProp values, though differences in fragment contributions were found, with nitrogen-bearing functional groups showing the largest variation between methods. Differences between methods showed how the calculation of the PSA is dependent on the method used and, therefore, judicious application of the upper limits used in the prediction of oral bioavailability is warranted. These results also indicate that, because of the differences in the way PSA values are calculated, values from the different methods should not be used interchangeably.
Anitha, R; Gunasekaran, M; Kumar, S Suresh; Athimoolam, S; Sridhar, B
2015-01-01
The common house hold pharmaceutical drug, paracetamol (PAR), has been synthesized from 4-chloroaniline as a first ever report. After the synthesis, good quality single crystals were obtained for slow evaporation technique under the room temperature. The crystal and molecular structures were re-determined by the single crystal X-ray diffraction. The vibrational spectral measurements were carried out using FT-IR and FT-Raman spectroscopy in the range of 4000-400 cm(-1). The single crystal X-ray studies shows that the drug crystallized in the monoclinic system polymorph (Form-I). The crystal packing is dominated by N-H⋯O and O-H⋯O classical hydrogen bonds. The ac diagonal of the unit cell features two chain C(7) and C(9) motifs running in the opposite directions. These two chain motifs are cross-linked to each other to form a ring R4(4)(22) motif and a chain C2(2)(6) motif which is running along the a-axis of the unit cell. Along with the classical hydrogen bonds, the methyl group forms a weak C-H⋯O interactions in the crystal packing. It offers the support for molecular assembly especially in the hydrophilic regions. Further, the strength of the hydrogen bonds are studied the shifting of vibrational bands. Geometrical optimizations of the drug molecule were done by the Density Functional Theory (DFT) using the B3LYP function and Hartree-Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which show significant agreement. The factor group analysis of the molecule was carried out by the various molecular symmetry, site and factor group species using the standard correlation method. The Natural Bond Orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and intramolecular charge transfer (ICT). The chemical softness, chemical hardness, electro-negativity, chemical potential and electrophilicity index of the molecule were found out first
SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN QUANTUM-CHEMICAL CALCULATIONS
DEVRIES, AH; VANDUIJNEN, PT; JUFFER, AH
1993-01-01
Recently we presented an extension of the direct reaction field (DRF) method, in which a quantum system and a set of point charges and interacting polarizabilities are embedded in a continuum that is characterized by a dielectric constant epsilon and a finite ionic strength. The reaction field of
SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN QUANTUM-CHEMICAL CALCULATIONS
DEVRIES, AH; VANDUIJNEN, PT; JUFFER, AH
1993-01-01
Recently we presented an extension of the direct reaction field (DRF) method, in which a quantum system and a set of point charges and interacting polarizabilities are embedded in a continuum that is characterized by a dielectric constant epsilon and a finite ionic strength. The reaction field of th
Riahi, Siavash; Beheshti, Abolghasem; Ganjali, Mohammad Reza; Norouzi, Parviz
2009-12-01
In this paper the relationship between the chemical structure and fluorescence characteristics of 30 phenylquinolinylethyne (PhQE), and phenylisoquinolinylethyne (PhIE) derivatives compounds employing ab initio calculations have been elucidated. Quantum chemical calculations (6-31G) were carried out to obtain: the optimized geometry, energy levels, charges and dipole moments of these compounds, in the singlet (steady and excited states) and triplet states. The relationship between quantum chemical descriptors, and wavelength of maximum excitation and emission indicated that these two parameters have the most correlation with quantum chemical hardness (eta). Also, stokes shift has the most correlation with the square of difference between the maximum of positive charges in the singlet steady and singlet excited states. The quantitative structure-property relationship (QSPR) of PhQE and PhIE was studied for relative fluorescence intensity (RFI). The genetic algorithm (GA) was applied to select the variables that resulted in the best-fit models. After the variable selection, multiple linear regression (MLR) and support vector machine (SVM) were both utilized to construct linear and non-linear QSPR models, respectively. The SVM model demonstrated a better performance than that of the MLR model. The route mean square error (RMSE) in the training and the test sets for the SVM model was 0.195 and 0.324, and the correlation coefficients were 0.965 and 0.960, respectively, thus revealing the reliability of this model. The resulting data indicated that SVM could be used as a powerful modeling tool for QSPR studies. According to the best of our knowledge, this is the first research on QSPR studies to predict RFI for a series of PhQE and PhIE derivative compounds using SVM.
Ghasemi, Amin; Asgarpour Khansary, Milad; Marjani, Azam; Shirazian, Saeed
2017-03-03
This paper is devoted to investigate the suitability of cellulose for estrogens micropollutants removal from water effluent. For this purpose, the sorption of eight estrogens including Estradiol, Estrone, Testosterone, Progesterone, Estriol, Mestranol, Ethinylestradiol and Diethylstilbestrol were investigated. The charge density profiles and sorption curves were obtained and discussed using quantum chemical calculations where the Accelrys Materials Studio software and COSMO-SAC model were employed. The geometry optimization of compound molecule and energy minimizations was performed using the Dmol3 Module and density functional theory of generalized gradient approximate and Volsko-Wilk-Nusair functional. We found that cellulose cannot be a reliable choice of sorbent for removal of Estrone and Estradiol, but it is a poor choice of sorbent for removal of Estriol, Ethinylestradiol. Cellulose can be used for Diethylstilbestrol, Mestranol, Testosterone and Progesterone removal from estrogens containing effluents.
Step-Scan FTIR spectroscopy and quantum chemical calculations of xanthone in the triplet state
Buschhaus, L.; Kleinermanns, K.
2014-10-01
Step-Scan-FTIR spectroscopy has been used to measure the infrared spectrum of xanthone in the triplet state using chloroform as solvent. Xanthone is an important triplet sensitizer and therefore suitable as model system. Xanthone was excited at 266 nm and its IR triplet spectrum measured in the range 1000-1750 cm-1. The spectrum was analyzed by comparison with DFT/B3LYP/TZVP/COSMO calculations. Further on the results were compared to gas phase IR measurements of triplet xanthone and calculations of isolated xanthone. Mainly based on the calculations we tried to identify the geometry changes from the electronic ground state to the first triplet state.
CBS-QB3 calculation of quantum chemical molecular descriptors of isomeric thiadiazoles.
Glossman-Mitnik, Daniel
2006-12-01
The results of the calculation of several molecular descriptors of isomeric thiadiazoles through the CBS-QB3 model chemistry are presented in this work. The results could be useful in quantitative structure-activity relationship (QSAR) or quantitative structure-property relationship (QSPR) studies of derivatives of the nitrogen-containing analogs of thiophene.
Development of Quantum Chemical Method to Calculate Half Maximal Inhibitory Concentration (IC50 ).
Bag, Arijit; Ghorai, Pradip Kr
2016-05-01
Till date theoretical calculation of the half maximal inhibitory concentration (IC50 ) of a compound is based on different Quantitative Structure Activity Relationship (QSAR) models which are empirical methods. By using the Cheng-Prusoff equation it may be possible to compute IC50 , but this will be computationally very expensive as it requires explicit calculation of binding free energy of an inhibitor with respective protein or enzyme. In this article, for the first time we report an ab initio method to compute IC50 of a compound based only on the inhibitor itself where the effect of the protein is reflected through a proportionality constant. By using basic enzyme inhibition kinetics and thermodynamic relations, we derive an expression of IC50 in terms of hydrophobicity, electric dipole moment (μ) and reactivity descriptor (ω) of an inhibitor. We implement this theory to compute IC50 of 15 HIV-1 capsid inhibitors and compared them with experimental results and available other QASR based empirical results. Calculated values using our method are in very good agreement with the experimental values compared to the values calculated using other methods.
Guirgis, Gamil A; Dukes, Horace W; Wyatt, Justin K; Nielsen, Claus J; Horn, Anne; Aleksa, Valdemaras; Klaeboe, Peter
2015-02-05
Raman spectra of 1,1-difluoro-1-silacyclohexane as a liquid, and as a solid at 78 K were recorded and depolarization data obtained. The infrared spectra of the vapour, liquid and amorphous and crystalline solids have been studied. In the low temperature IR and Raman spectra eight and three bands, respectively, were shifted a few cm(-1) when the sample crystallized. No bands vanished after crystallization in agreement with the assumption that only one conformer (chair) was present in all the states of aggregation. The compound exists in the stable chair conformation, whereas in the parent silacyclohexane a possible twist form should have more than 15 kJ mol(-1) higher energies than the chair, as derived from various calculations. The wavenumbers of the vibrational modes were calculated in the harmonic and anharmonic approximation employing B3LYP/cc-pVTZ calculations. The 27 A' and 21 A″ fundamentals were assigned on the basis of the calculations, infrared vapour contours, Raman depolarization measurements and infrared and Raman band intensities. An average, relative deviation of 1.5% was found between the observed and the anharmonic wavenumbers for the 48 modes.
Quantum chemical calculations using the Floating Point Systems, Inc. Model 164 attached processor
Energy Technology Data Exchange (ETDEWEB)
Shepard, R.; Bair, R.A.; Eades, R.A.; Wagner, A.F.; Davis, M.J.; Harding, L.B.; Dunning, T.H. Jr.
1983-01-01
The Theoretical Chemistry Group at Argonne National Laboratory has had a Floating Point System, Inc., Model 164 Attached Processor (FPS-164) for several months. Actual production calculations, as well as benchmark calculations, indicate that the FPS-164 is capable of performance comparable to large mainframe computers, the groups experience with the FPS-164 includes the conversion of a complete system of electronic structure codes, including integral evaluation programs, generalized valence bond programs, integral transformation programs, and unitary group configuration interaction programs, and two classical trajectory codes. Timings of these programs at various levels of optimization along with estimates of the amount of effort required to make the necessary program modifications are discussed. 10 references, 2 figures, 2 tables.
N. S. Labidi
2013-01-01
The semiempirical AM1 SCF method is used to study the first static hyperpolarizabilities β of some novel mono-O-Hydroxy bidentate Schiff base in which electron donating (D) and electron accepting (A) groups were introduced on either side of the Schiff base ring system. Geometries of all molecules were optimized at the semiempirical AM1. The first static hyperpolarizabilities of these molecules were calculated using Hyperchem package. To understand this phenomenon in the context of molecular o...
Energy Technology Data Exchange (ETDEWEB)
Federico Jimenez-Cruz; Georgina C. Laredo [Instituto Mexicano del Petroleo, Mexico (Mexico). Programa de Tratamiento de Crudo Maya
2004-11-01
A good approach of the critical molecular dimensions of 35 linear and branched C5-C8 paraffins by DFT quantum chemical calculations at B3LYP/6-31G{asterisk}{asterisk} level of theory in gas phase is described. In this context, we found that either the determined molecular width or width-height average values can be used as critical measures in the analysis for selection of molecular sieves materials, depending on their pore size and shape. The molecular width values for linear and monosubstituted paraffins are 4.2 and 5.5 {angstrom}, respectively. In the case of disubstituted paraffins, the values are 5.5 for 2,3-, 2,4-, 2,5- and 3,4-disubstituted and for 2,2- and 3,3-disubstituted are 6.7-7.1 {angstrom}. The values for ethyl-substituted are 6.1-6.7 {angstrom} and for trisubstituted isoparaffins are 6.7. In order to select a porous material for selective separation of isoparaffins and paraffins, the zeolite diffusivity can be correlated with the critical diameter of the paraffins according to the geometry-limited diffusion concept and the effective minimum dimensions of the molecules. The calculated values of CPK molecular volume of the titled paraffins showed a good discrimination between the number of carbons and molecular size. 25 refs., 4 figs., 2 tabs.
Leang, Sarom S; Rendell, Alistair P; Gordon, Mark S
2014-03-11
Increasingly, modern computer systems comprise a multicore general-purpose processor augmented with a number of special purpose devices or accelerators connected via an external interface such as a PCI bus. The NVIDIA Kepler Graphical Processing Unit (GPU) and the Intel Phi are two examples of such accelerators. Accelerators offer peak performances that can be well above those of the host processor. How to exploit this heterogeneous environment for legacy application codes is not, however, straightforward. This paper considers how matrix operations in typical quantum chemical calculations can be migrated to the GPU and Phi systems. Double precision general matrix multiply operations are endemic in electronic structure calculations, especially methods that include electron correlation, such as density functional theory, second order perturbation theory, and coupled cluster theory. The use of approaches that automatically determine whether to use the host or an accelerator, based on problem size, is explored, with computations that are occurring on the accelerator and/or the host. For data-transfers over PCI-e, the GPU provides the best overall performance for data sizes up to 4096 MB with consistent upload and download rates between 5-5.6 GB/s and 5.4-6.3 GB/s, respectively. The GPU outperforms the Phi for both square and nonsquare matrix multiplications.
Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations
Liao, Rong-Zhen; Yu, Jian-Guo; Himo, Fahmi
2010-01-01
Acetylene hydratase is a tungsten-dependent enzyme that catalyzes the nonredox hydration of acetylene to acetaldehyde. Density functional theory calculations are used to elucidate the reaction mechanism of this enzyme with a large model of the active site devised on the basis of the native X-ray crystal structure. Based on the calculations, we propose a new mechanism in which the acetylene substrate first displaces the W-coordinated water molecule, and then undergoes a nucleophilic attack by the water molecule assisted by an ionized Asp13 residue at the active site. This is followed by proton transfer from Asp13 to the newly formed vinyl anion intermediate. In the subsequent isomerization, Asp13 shuttles a proton from the hydroxyl group of the vinyl alcohol to the α-carbon. Asp13 is thus a key player in the mechanism, but also W is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Several other mechanisms are also considered but the energetic barriers are found to be very high, ruling out these possibilities. PMID:21149684
Vibrational spectra, DFT quantum chemical calculations and conformational analysis of P-iodoanisole.
Arivazhagan, M; Anitha Rexalin, D; Geethapriya, J
2013-09-01
The solid phase FT-IR and FT-Raman spectra of P-iodoanisole (P-IA) have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by ab initio (HF) and density functional theory (B3LYP) methods with LanL2DZ as basis set. The potential energy surface scan for the selected dihedral angle of P-IA has been performed to identify stable conformer. The optimized structure parameters and vibrational wavenumbers of stable conformer have been predicted by density functional B3LYP method with LanL2DZ (with effective core potential representations of electrons near the nuclei for post-third row atoms) basis set. The nucleophilic and electrophilic sites obtained from the molecular electrostatic potential (MEP) surface were calculated. The temperature dependence of thermodynamic properties has been analyzed. Several thermodynamic parameters have been calculated using B3LYP with LanL2DZ basis set.
Suess, Christian J; Hirst, Jonathan D; Besley, Nicholas A
2017-04-01
The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two-dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time-dependent density functional theory. Key intermediate residues between the donor and acceptor are identified, and in particular the residues Val68 and Ile75 play a critical role in calculations of the electron coupling matrix elements. Our calculations demonstrate how small changes in structure can have a large effect on the rates, and show that the different rates of electron transfer are dictated by the distance between the heme and tryptophan residues, while for excitation energy transfer the orientation of the tryptophan residues relative to the heme is important. © 2017 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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N. S. Labidi
2013-01-01
Full Text Available The semiempirical AM1 SCF method is used to study the first static hyperpolarizabilities β of some novel mono-O-Hydroxy bidentate Schiff base in which electron donating (D and electron accepting (A groups were introduced on either side of the Schiff base ring system. Geometries of all molecules were optimized at the semiempirical AM1. The first static hyperpolarizabilities of these molecules were calculated using Hyperchem package. To understand this phenomenon in the context of molecular orbital picture, we examined the molecular HOMO and molecular LUMO generated via Hyperchem. The study reveals that the mono-O-Hydroxy bidentate Schiff bases have large β values and hence in general may have potential applications in the development of nonlinear optical materials.
Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.
2016-05-01
The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.
Energy Technology Data Exchange (ETDEWEB)
Chavda, Bhavin R., E-mail: chavdabhavin9@gmail.com; Dubey, Rahul P.; Patel, Urmila H. [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120, Gujarat (India); Gandhi, Sahaj A. [Bhavan’s Shri I.L. Pandya Arts-Science and Smt. J.M. shah Commerce College, Dakar, Anand -388001, Gujarat, Indian (India); Barot, Vijay M. [P. G. Center in Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat 383 215 (India)
2016-05-06
The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb –London –Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.
Lifshitz, Assa; Tamburu, Carmen; Dubnikova, Faina
2008-02-07
The reactions of 1-naphthyl radicals with ethylene were studied behind reflected shock waves in a single pulse shock tube, covering the temperature range 950-1200 K at overall densities behind the reflected shocks of approximately 2.5 x 10(-5) mol/cm3. 1-Iodonaphthalene served as the source for 1-naphthyl radicals as its C-I bond dissociation energy is relatively small. It is only approximately 65 kcal/mol as compared to the C-H bond strength in naphthalene which is approximately 112 kcal/mol and can thus produce naphthyl radicals at rather low reflected shock temperatures. The [ethylene]/[1-iodo-naphthalene] ratio in all of the experiments was approximately 100 in order to channel the free radicals into reactions with ethylene rather than iodonaphthalene. Four products resulting from the reactions of 1-naphthyl radicals with ethylene were found in the post shock samples. They were vinyl naphthalene, acenaphthene, acenaphthylene, and naphthalene. Some low molecular weight aliphatic products at rather low concentrations, resulting from the attack of various free radicals on ethylene were also found in the shocked samples. In view of the relatively low temperatures employed in the present experiments, the unimolecular decomposition rate of ethylene is negligible. Three potential energy surfaces describing the production of vinyl naphthalene, acenaphthene, and acenaphthylene were calculated using quantum chemical methods and rate constants for the elementary steps on the surfaces were calculated using transition state theory. Naphthalene is not part of the reactions on the surfaces. Acenaphthylene is obtained only from acenaphthene. A kinetics scheme containing 27 elementary steps most of which were obtained from the potential energy surfaces was constructed and computer modeling was performed. An excellent agreement between the experimental yields of the four major products and the calculated yields was obtained.
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Luis Enrique Gómez-Pineda
2010-06-01
Full Text Available Quantum chemical calculations were performed to characterize the interaction of the flavonol molecule (FL with methacrylic acid (MAA and 4-vinylpyridine (4VPy in the formation of imprinted polymers. The polarizable continuum model (PCM was used to gain insight on the type of interaction between the reactant molecules under vacuum conditions and in the presence of different solvents. The effect of solvent on the pre-polymerization complex formation was evaluated through the stability energy, in which chloroform behaves as the best solvent for the synthesis of the imprinted polymers since it facilitates the reaction by lowering its degree of stabilization. The reactivity was analyzed in terms of the electrostatic surface potential (ESP and Mulliken charge. By means of these results, it has been possible to determine two potential recognition sites for the interaction of the MAA monomer and one for the 4VPy in relation to the strength of interaction with FL. In this concern, the interaction of the system FL-MAA is stronger than FL-4VPy.
Gao, Ting; Shi, Li-Li; Li, Hai-Bin; Zhao, Shan-Shan; Li, Hui; Sun, Shi-Ling; Su, Zhong-Min; Lu, Ying-Hua
2009-07-07
The combination of genetic algorithm and back-propagation neural network correction approaches (GABP) has successfully improved the calculation accuracy of absorption energies. In this paper, the absorption energies of 160 organic molecules are corrected to test this method. Firstly, the GABP1 is introduced to determine the quantitative relationship between the experimental results and calculations obtained by using quantum chemical methods. After GABP1 correction, the root-mean-square (RMS) deviations of the calculated absorption energies reduce from 0.32, 0.95 and 0.46 eV to 0.14, 0.19 and 0.18 eV for B3LYP/6-31G(d), B3LYP/STO-3G and ZINDO methods, respectively. The corrected results of B3LYP/6-31G(d)-GABP1 are in good agreement with experimental results. Then, the GABP2 is introduced to determine the quantitative relationship between the results of B3LYP/6-31G(d)-GABP1 method and calculations of the low accuracy methods (B3LYP/STO-3G and ZINDO). After GABP2 correction, the RMS deviations of the calculated absorption energies reduce to 0.20 and 0.19 eV for B3LYP/STO-3G and ZINDO methods, respectively. The results show that the RMS deviations after GABP1 and GABP2 correction are similar for B3LYP/STO-3G and ZINDO methods. Thus, the B3LYP/6-31G(d)-GABP1 is a better method to predict absorption energies and can be used as the approximation of experimental results where the experimental results are unknown or uncertain by experimental method. This method may be used for predicting absorption energies of larger organic molecules that are unavailable by experimental methods and by high-accuracy theoretical methods with larger basis sets. The performance of this method was demonstrated by application to the absorption energy of the aldehyde carbazole precursor.
Effectively calculable quantum mechanics
Bolotin, Arkady
2015-01-01
According to mathematical constructivism, a mathematical object can exist only if there is a way to compute (or "construct") it; so, what is non-computable is non-constructive. In the example of the quantum model, whose Fock states are associated with Fibonacci numbers, this paper shows that the mathematical formalism of quantum mechanics is non-constructive since it permits an undecidable (or effectively impossible) subset of Hilbert space. On the other hand, as it is argued in the paper, if...
Welsch, Ralph; Manthe, Uwe
2014-08-07
The mode-selective chemistry of the title reaction is studied by full-dimensional quantum dynamics simulation on an accurate ab initio potential energy surface for vanishing total angular momentum. Using a rigorous transition state based approach and multi-configurational time-dependent Hartree wave packet propagation, initial state-selected reaction probabilities for many ro-vibrational states of methane are calculated. The theoretical results are compared with experimental trends seen in reactions of methane. An intuitive interpretation of the ro-vibrational control of the chemical reactivity provided by a sudden model based on the quantum transition state concept is discussed.
Koparir, Pelin; Sarac, Kamiran; Orek, Cahit; Koparir, Metin
2016-11-01
This study acquaints the 8-t-buthyl-4-methyl-2H-chromen 2-one (II) of by quantum chemical calculations and spectral ways. The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of II in the ground state have been calculated utilizing the density functional method (B3LYP) with the 6-31G(d) basis set. The theoretical vibrational frequencies and chemical shift values display well agreement with experimental values. On the other hand, DFT calculations of molecular electrostatic potentials and frontier molecular orbitals of II were implemented at the B3LYP/6-31G(d) level of theory.
Ksenafontov, Denis N.; Moiseeva, Natalia F.; Khristenko, Lyudmila V.; Karasev, Nikolai M.; Shishkov, Igor F.; Vilkov, Lev V.
2010-12-01
The geometric structure of piracetam was studied by quantum chemical calculations (DFT and ab initio), gas electron diffraction (GED), and FTIR spectroscopy. Two stable mirror symmetric isomers of piracetam were found. The conformation of pyrrolidine ring is an envelope in which the C4 atom deviates from the ring plane, the angle between the planes (C3 sbnd C4 sbnd C5) and (C2 sbnd C3 sbnd C5) is 154.1°. The direction of the deviation is the same as that of the side acetamide group. The piracetam molecule is stabilized in the gas phase by an intramolecular hydrogen bond between the N9H 2 group and the oxygen O6, bonded to C2. The principal structural parameters ( re, Å and ∠e, degrees; uncertainties are 3 σLS values) were found to be: r(С3 sbnd С4) = 1.533(1), r(C4 sbnd C5) = 1.540(1), r(N1 sbnd C5) = 1.456(1), r(C2 sbnd C3) = 1.520(1), r(N1 sbnd C7) = 1.452(1), r(C7 sbnd C8) = 1.537(1), r(N1 sbnd C2) = 1.365(2), r(C8 sbnd N9) = 1.360(2), r(C2 dbnd O6) = 1.229(1), r(C8 dbnd O10) = 1.221(1), ∠C2 sbnd N1 sbnd C5 = 113.4(6), ∠N1 sbnd C2 sbnd C3 = 106.9(6), ∠N1 sbnd C7 sbnd C8 = 111.9(6), ∠C7 sbnd C8 sbnd N9 = 112.5(6), ∠N1 sbnd C2 sbnd O6 = 123.0(4), ∠C3 sbnd N1 sbnd C7 = 120.4(4), ∠C7 sbnd C8 sbnd O10 = 120.2(4), ∠C5 sbnd N1 sbnd C2 sbnd O6 = 170(6), ∠C3 sbnd C2 sbnd N1 sbnd C7 = 178(6), ∠C2 sbnd N1 sbnd C7 sbnd C8 = 84.2, ∠N1 sbnd C7 sbnd C8 sbnd O10 = 111.9.
Institute of Scientific and Technical Information of China (English)
ZHANG Jing; YANG Bing-Qin; ZHU Hai-Yan; LI Tao; WEN Zhen-Yi
2006-01-01
A novel benzimidazole derivative, 1,3-dimethyl-2-ferrocenylmethylbenzimidazolium iodide (1) was synthesized and characterized by elemental analysis, MS, 1H NMR and IR spectra. Its crystal structure was determined by X-ray single crystal diffraction, and the title compound belongs to monoclinic system with space group P2(1)/c.According to the crystal structure, the quantum chemistry calculation was performed by Gaussian 03 program, and full geometry optimizations of the title compound were carried out with DFT method at B3LYP/6-31G level. Its structure, stability, frontier molecular orbital components and net charge distribution were discussed.
Minyaev, Ruslan M.; Quapp, Wolfgang; Schmidt, Benjamin; Getmanskii, Ilya V.; Koval, Vitaliy V.
2013-11-01
Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the SN2 nucleophile substitution reactions CH4 + H- → CH4 + H- and CH4 + F- → CH3F + H-. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.
Shlykov, Sergey A.; Phien, Tran D.; Gao, Yan; Weber, Peter M.
2017-03-01
Molecular structure and conformational behavior of N-phenylpiperidine (NPhP) were investigated by synchronous gas-phase electron diffraction/mass spectrometry (GED/MS) and quantum chemistry. Due to influence of steric repulsion and hyperconjugation, NPhP may exist in two conformers, equatorial and axial chair forms. Both experiment and theoretical calculations suggest a C1 symmetry of the conformers, with the plane perpendicular to the phenyl group turned by ca. 30-40° (equatorial) and 0-20° (axial) about the plane perpendicular to the piperidine ring symmetry plane. According to the QC calculations, NPhP may exist as two conformers, equatorial and axial, with a ratio of Eq:Ax = 92:8 (B3LYP), 87:13 (B3LYP-GD3), 84:16 (M06-2X), 83:17 (MP2/6-311G**) and 76:24% (MP2/cc-pVTZ). Except for the latter, these values are in good agreement with the experimental GED data of 90(10):10(10)%. A comparative analysis of similar compounds, phenylcyclohexane and 1-phenylheterocyclohexanes, was performed. Conformational properties depend on the CPhsbnd X bond distance and hyperconjugation between the phenyl ring and the lone pair on the heteroatom. The contribution of the axial form of 1-phenylcyclohexane derivatives increases in the series of the heteroatom X in the cyclohexane ring: C → N → Si → P.
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Jun Hu
2015-01-01
Full Text Available The inhibition mechanism of thiourea (TU and hexamethylenetetramine (HMTA mixed in 15% HCl solution on N80 surface was investigated by potentiodynamic polarization, electrochemical impedance spectroscopy measurements, and surface morphology analysis. Quantum chemical calculations and molecular dynamics simulations were performed to study the properties of TU and HMTA. The results showed that the inhibitors can form strong bonds and stable films on the surface, which inhibits the cathodic and anodic reactions in HCl solution and reduces the diffusion coefficients of corrosive particles.
Arivazhagan, G; Shanmugam, R; Elangovan, A
2013-03-15
The results of FTIR spectral measurement on equimolar diisopropyl ether-butyric acid binary mixture and quantum chemical calculations on the complex molecule have been presented. Dielectric studies have been carried out on the binary mixture over the entire composition range and at four different temperatures 303 K, 308 K, 313 K and 318 K. n-Butyric acid seems to prefer less polar ether to interact with it. It appears that the usual interpretation of variation of static dielectric constant and positive deviation of excess permittivity from ideal mixture behavior needs to be relooked.
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Voloshina, E.N.; Raabe, G.; Fleischhauer, J.; Kramp, G.J.; Gais, H.J. [Rheinisch-Westfaelische Technische Hochschule Aachen (Germany). Inst. fuer Organische Chemie
2004-07-01
The chiroptical properties of the diastereomeric alcohols (E)-(3S,4S)-4-methyl-1-tributylstannyl-oct-1-en-6-yn-3-ol ((S,S)-3) and (E)-(3R,4S)-4-methyl-1-tributylstannyl-oct-1-en-6-yn-3-ols ((R,S)-3) have been studied experimentally as well as by quantum-chemical calculations. The structures of 20 conformers of each isomer, which were found to represent local minima at the MNDO level, have been optimized with density functional theory (DFT). Based on these geometries the excitation energies and oscillator as well as rotational strengths have been calculated using a time-dependent DFT (TDDFT) method. The CD spectra of the compounds were then obtained as superposition of Boltzmann-weighted spectra for each of the structures. By comparison of the calculated and the experimental CD spectra the absolute configurations have been assigned to the investigated compounds. (orig.)
Voloshina, E. N.; Raabe, G.; Fleischhauer, J.; Kramp, G. J.; Gais, H.-J.
2004-03-01
The chiroptical properties of the diastereomeric alcohols (E)-(3S,4S)-4-methyl-1-tributylstannyloct- 1-en-6-yn-3-ol ((S,S)-) and (E)-(3R,4S)-4-methyl-1-tributylstannyl-oct-1-en-6-yn-3-ols ((R,S)- 3) have been studied experimentally as well as by quantum-chemical calculations. The structures of 20 conformers of each isomer, which were found to represent local minima at the MNDO level, have been optimized with density functional theory (DFT). Based on these geometries the excitation energies and oscillator as well as rotational strengths have been calculated using a time-dependent DFT (TDDFT) method. The CD spectra of the compounds were then obtained as superposition of Boltzmann-weighted spectra for each of the structures. By comparison of the calculated and the experimental CD spectra the absolute configurations have been assigned to the investigated compounds.
Alam, Mohammad Jane; Ahmad, Shabbir
2015-02-05
FTIR, FT-Raman and electronic spectra of allantoin molecule are recorded and investigated using DFT and MP2 methods with 6-311++G(d,p) basis set. The molecular structure, anharmonic vibrational spectra, natural atomic charges, non-linear optical properties, etc. have been computed for the ground state of allantoin. The anharmonic vibrational frequencies are calculated using PT2 algorithm (Barone method) as well as VSCF and CC-VSCF methods. These methods yield results that are in remarkable agreement with the experiment. The coupling strengths between pairs of modes are also calculated using coupling integral based on 2MR-QFF approximation. The simulations on allantoin dimers have been also performed at B3LYP/6-311++G(d,p) level of theory to investigate the effect of the intermolecular interactions on the molecular structure and vibrational frequencies of the monomer. Vibrational assignments are made with the great accuracy using PED calculations and animated modes. The combination and overtone bands have been also identified in the FTIR spectrum with the help of anharmonic computations. The electronic spectra are simulated in gas and solution at TD-B3LYP/6-311++G(d,p) level of theory. The important global quantities such as electro-negativity, electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO, LUMO energy eigenvalues are also computed. NBO analysis has been performed for monomer and dimers of allantoin at B3LYP/6-311++G(d,p) level of theory. Copyright © 2014 Elsevier B.V. All rights reserved.
Sangeetha, V; Govindarajan, M; Kanagathara, N; Marchewka, M K; Gunasekaran, S; Anbalagan, G
2014-05-05
Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted.
Ouksel, Louiza; Chafaa, Salah; Bourzami, Riadh; Hamdouni, Noudjoud; Sebais, Miloud; Chafai, Nadjib
2017-09-01
Single Diethyl [hydroxy (phenyl) methyl] phosphonate (DHPMP) crystal with chemical formula C11H17O4P, was synthesized via the base-catalyzed Pudovik reaction and Lewis acid as catalyst. The results of SXRD analyzes indicate that this compound crystallizes into a mono-clinic system with space group P21/n symmetry and Z = 4. The crystal structure parameters are a = 9.293 Å, b = 8.103 Å, c = 17.542 Å, β = 95.329° and V = 1315.2 Å3, the structure displays one inter-molecular O-H⋯O hydrogen bonding. The UV-Visible absorption spectrum shows that the crystal exhibits a good optical transmission in the visible domain, and strong absorption in middle ultraviolet one. The vibrational frequencies of various functional groups present in DHPMP crystal have been deduced from FT-IR and FT-Raman spectra and then compared with theoretical values performed with DFT (B3LYP) method using 6-31G (p, d) basis sets. Chemical and thermodynamic parameters such as: ionization potential (I), electron affinity (A), hardness (σ), softness (η), electronegativity (χ) and electrophilicity index (ω), are also calculated using the same theoretical method. The thermal decomposition behavior of DHPMP, studied by using thermogravimetric analysis (TDG), shows a thermal stability until to 125 °C.
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Masego Dibetsoe
2015-08-01
Full Text Available The effects of seven macrocyclic compounds comprising four phthalocyanines (Pcs namely 1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (Pc1, 2,3,9,10,16,17,23,24-octakis(octyloxy-29H,31H-phthalocyanine (Pc2, 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (Pc3 and 29H,31H-phthalocyanine (Pc4, and three naphthalocyanines namely 5,9,14,18,23,27,32,36-octabutoxy-2,3-naphthalocyanine (nPc1, 2,11,20,29-tetra-tert-butyl-2,3-naphthalocyanine (nPc2 and 2,3-naphthalocyanine (nP3 were investigated on the corrosion of aluminium (Al in 1 M HCl using a gravimetric method, potentiodynamic polarization technique, quantum chemical calculations and quantitative structure activity relationship (QSAR. Synergistic effects of KI on the corrosion inhibition properties of the compounds were also investigated. All the studied compounds showed appreciable inhibition efficiencies, which decrease with increasing temperature from 30 °C to 70 °C. At each concentration of the inhibitor, addition of 0.1% KI increased the inhibition efficiency compared to the absence of KI indicating the occurrence of synergistic interactions between the studied molecules and I− ions. From the potentiodynamic polarization studies, the studied Pcs and nPcs are mixed type corrosion inhibitors both without and with addition of KI. The adsorption of the studied molecules on Al surface obeys the Langmuir adsorption isotherm, while the thermodynamic and kinetic parameters revealed that the adsorption of the studied compounds on Al surface is spontaneous and involves competitive physisorption and chemisorption mechanisms. The experimental results revealed the aggregated interactions between the inhibitor molecules and the results further indicated that the peripheral groups on the compounds affect these interactions. The calculated quantum chemical parameters and the QSAR results revealed the possibility of strong interactions between the studied inhibitors and metal surface. QSAR
Dibetsoe, Masego; Olasunkanmi, Lukman O; Fayemi, Omolola E; Yesudass, Sasikumar; Ramaganthan, Baskar; Bahadur, Indra; Adekunle, Abolanle S; Kabanda, Mwadham M; Ebenso, Eno E
2015-08-28
The effects of seven macrocyclic compounds comprising four phthalocyanines (Pcs) namely 1,4,8,11,15,18,22,25-octabutoxy-29H,31H-phthalocyanine (Pc1), 2,3,9,10,16,17,23,24-octakis(octyloxy)-29H,31H-phthalocyanine (Pc2), 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (Pc3) and 29H,31H-phthalocyanine (Pc4), and three naphthalocyanines namely 5,9,14,18,23,27,32,36-octabutoxy-2,3-naphthalocyanine (nPc1), 2,11,20,29-tetra-tert-butyl-2,3-naphthalocyanine (nPc2) and 2,3-naphthalocyanine (nP3) were investigated on the corrosion of aluminium (Al) in 1 M HCl using a gravimetric method, potentiodynamic polarization technique, quantum chemical calculations and quantitative structure activity relationship (QSAR). Synergistic effects of KI on the corrosion inhibition properties of the compounds were also investigated. All the studied compounds showed appreciable inhibition efficiencies, which decrease with increasing temperature from 30 °C to 70 °C. At each concentration of the inhibitor, addition of 0.1% KI increased the inhibition efficiency compared to the absence of KI indicating the occurrence of synergistic interactions between the studied molecules and I(-) ions. From the potentiodynamic polarization studies, the studied Pcs and nPcs are mixed type corrosion inhibitors both without and with addition of KI. The adsorption of the studied molecules on Al surface obeys the Langmuir adsorption isotherm, while the thermodynamic and kinetic parameters revealed that the adsorption of the studied compounds on Al surface is spontaneous and involves competitive physisorption and chemisorption mechanisms. The experimental results revealed the aggregated interactions between the inhibitor molecules and the results further indicated that the peripheral groups on the compounds affect these interactions. The calculated quantum chemical parameters and the QSAR results revealed the possibility of strong interactions between the studied inhibitors and metal surface. QSAR analysis on the
Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro
2013-09-01
Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.
Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro
2013-09-01
Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as "pau branco". Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The (13)C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d,p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.
Mishra, H.; Colussi, A. J.; Enami, S.; Nielsen, R. J.; Hoffmann, M. R.; Goddard, W. A.
2012-12-01
It has become increasingly apparent that atmospheric chemistry involves more than gas-phase reactions. Key processes, such as the decay of NO2 in urban plumes and the associated daytime formation of HONO, and the rapid chemistries observed in and over forest canopies at nighttime defy explanation by conventional atmospheric chemistry mechanisms. We have recently reported experimental results on several gas-liquid reactions of atmospheric interest, such as the facile protonation of gaseous isoprene on mildly acidic (pH bioenergetics coupling, 'on-water' catalysis, self-assembly and molecular recognition, little is known about the molecular mechanisms of such reactions. Herein we apply quantum mechanics to investigate how biogenic or anthropogenic olefins may get protonated and undergo oligomerization at the air-water interface by performing model calculations on small water clusters carrying an excess proton as surrogates for the surface of mildly acidic water as sensed by gaseous isoprene (ISO). We find that ISO binds weakly to the surface of water and accepts a proton from H+(H2O)3, leading to ISOH+ via a proton transfer hindered by a ΔG1‡ = 5.6 kcal mol-1 kinetic barrier. Subsequently, another ISO attaches loosely to this ensemble, before being attacked by the ISOH+. This process, which represents the first step of the cationic polymerization of ISO, is hindered by a similar ΔG2‡ = 5.7 kcal mol-1 barrier. Our theoretical results are consistent with experimental (~ 10-4) uptake coefficients for ISO measured on acidic water.
Directory of Open Access Journals (Sweden)
Višňak Jakub
2016-01-01
Full Text Available A brief introduction into computational methodology and preliminary results for spectroscopic (excitation energies, vibrational frequencies in ground and excited electronic states and thermodynamic (stability constants, standard enthalpies and entropies of complexation reactions properties of some 1:1, 1:2 and 1:3 uranyl sulphato- and selenato- complexes in aqueos solutions will be given. The relativistic effects are included via Effective Core Potential (ECP, electron correlation via (TDDFT/B3LYP (dispersion interaction corrected and solvation is described via explicit inclusion of one hydration sphere beyond the coordinated water molecules. We acknowledge limits of this approximate description – more accurate calculations (ranging from semi-phenomenological two-component spin-orbit coupling up to four-component Dirac-Coulomb-Breit hamiltonian and Molecular Dynamics simulations are in preparation. The computational results are compared with the experimental results from Time-resolved Laser-induced Fluorescence Spectroscopy (TRLFS and UV-VIS spectroscopic studies (including our original experimental research on this topic. In case of the TRLFS and UV-VIS speciation studies, the problem of complex solution spectra decomposition into individual components is ill-conditioned and hints from theoretical chemistry could be very important. Qualitative agreement between our quantum chemical calculations of the spectroscopic properties and experimental data was achieved. Possible applications for geochemical modelling (e.g. safety studies of nuclear waste repositories, modelling of a future mining site and analytical chemical studies (including natural samples are discussed.
Višňak, Jakub; Sobek, Lukáš
2016-11-01
A brief introduction into computational methodology and preliminary results for spectroscopic (excitation energies, vibrational frequencies in ground and excited electronic states) and thermodynamic (stability constants, standard enthalpies and entropies of complexation reactions) properties of some 1:1, 1:2 and 1:3 uranyl sulphato- and selenato- complexes in aqueos solutions will be given. The relativistic effects are included via Effective Core Potential (ECP), electron correlation via (TD)DFT/B3LYP (dispersion interaction corrected) and solvation is described via explicit inclusion of one hydration sphere beyond the coordinated water molecules. We acknowledge limits of this approximate description - more accurate calculations (ranging from semi-phenomenological two-component spin-orbit coupling up to four-component Dirac-Coulomb-Breit hamiltonian) and Molecular Dynamics simulations are in preparation. The computational results are compared with the experimental results from Time-resolved Laser-induced Fluorescence Spectroscopy (TRLFS) and UV-VIS spectroscopic studies (including our original experimental research on this topic). In case of the TRLFS and UV-VIS speciation studies, the problem of complex solution spectra decomposition into individual components is ill-conditioned and hints from theoretical chemistry could be very important. Qualitative agreement between our quantum chemical calculations of the spectroscopic properties and experimental data was achieved. Possible applications for geochemical modelling (e.g. safety studies of nuclear waste repositories, modelling of a future mining site) and analytical chemical studies (including natural samples) are discussed.
SOME QUANTUM CHEMICAL STUDY ON THE STRUCTURAL ...
African Journals Online (AJOL)
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Formula. Formula weight. (gmol-1) ... Quantum chemical calculations (Density Functional Theory, B3LYP/6-31G (d)) were used to purposed the ... correlation functional [B3LYP/6-31G(d)]) calculations were done by using Gaussian 03 program ...
Lee, Sung Keun; Stebbins, Jonathan F.
2006-08-01
Estimation of the framework connectivity and the atomic structure of depolymerized silicate melts and glasses (NBO/T > 0) remains a difficult question in high-temperature geochemistry relevant to magmatic processes and glass science. Here, we explore the extent of disorder and the nature of polymerization in binary Ca-silicate and ternary Ca-aluminosilicate glasses with varying NBO/T (from 0 to 2.67) using O-17 NMR at two different magnetic fields of 9.4 and 14.1 T in conjunction with quantum chemical calculations. Non-random distributions among framework cations (Si and Al) are demonstrated in the variation of relative populations of oxygen sites with NBO/T. The proportion of non-bridging oxygen (NBO, Ca-O-Si) in the binary and ternary aluminosilicate glasses increases with NBO/T. While the trend is consistent with predictions from composition, the detailed fractions apparently deviate from the predicted values, suggesting further complications in the nature of polymerization. The proportion of each bridging oxygen in the glasses also varies with NBO/T. The fractions of Al-O-Si and Al-O-Al increase with increasing polymerization as CaO is replaced with Al 2O 3, while that of Si-O-Si seems to decrease, implying that activity of silica may decrease from calcium silicate to polymerized aluminosilicates (X=constant). Quantum chemical molecular orbital calculations based on density functional theory show that a silicate chain with Al-NBO (Ca-O-Al) has an energy penalty (calculated cluster energy difference) of about 108 kJ/mol compared with the cluster with Ca-O-Si, consistent with preferential depolymerization of Si-networks, reported in an earlier O-17 NMR study [Allwardt, J., Lee, S.K., Stebbins, J.F., 2003. Bonding preferences of non-bridging oxygens in calcium aluminosilicate glass: Evidence from O-17 MAS and 3QMAS NMR on calcium aluminate glass. Am. Mineral.88, 949-954]. These prominent types of non-randomness in the distributions suggest significant chemical
Baltrusaitis, Jonas; Schuttlefield, Jennifer; Jensen, Jan H; Grassian, Vicki H
2007-09-28
Surface reactions of nitrogen oxides with aluminium oxide particles result in the formation of adsorbed nitrate. Specifically, when alpha-Al(2)O(3) and gamma-Al(2)O(3) particles are exposed to gas-phase NO(2) and HNO(3) adsorbed nitrate forms on the surface. In this study, Fourier transform infrared (FTIR) spectroscopy is combined with quantum chemical calculations to further our understanding of the adsorbed nitrate product on aluminium oxide particle surfaces in the presence and absence of co-adsorbed water at 296 K. FTIR spectra of adsorbed nitrate on alpha-Al(2)O(3) and gamma-Al(2)O(3) particles are interpreted using calculated vibrational frequencies of nitrate coordinated to binuclear Al oxide cluster models. Comparison of the calculated and experimental vibrational frequencies of adsorbed nitrate establishes different modes of coordination (monodentate, bidentate and bridging) of the nitrate ion to the surface in the absence of adsorbed water. In the presence of co-adsorbed water, the nitrate ion becomes fully solvated, as shown by a comparison of the experimental nitrate infrared spectra as a function of relative humidity with the calculated nitrate vibrational frequencies for binuclear Al cluster compounds which contain both coordinated nitrate ions and water molecules. These calculations also suggest that adsorbed water can displace nitrate from direct coordination to the surface, leading to an outer-sphere nitrate adsorption complex as well as an inner-sphere complex. Furthermore, the relative humidity dependence of the spectra suggest that water does not evenly wet the surface even at high relative humidity, as there are open or bare surface sites where nitrate ions are not solvated. Besides adsorbed mondendate, bidendate, bridging and solvated nitrate, the presence of ion bound nitrate ion, partially solvated nitrate, molecular nitric acid, hydronium ion and H(3)O(+):NO(3)(-) ion pairs on the oxide surface are also discussed.
Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun
2011-05-14
We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.
Fossgård, Eirik; Ruud, Kenneth
2006-02-01
We describe the implementation of a parallel, in-core, integral-direct Hartree-Fock and density functional theory code for the efficient calculation of Hartree-Fock wave functions and density functional theory. The algorithm is based on a parallel master-slave algorithm, and the two-electron integrals calculated by a slave are stored in available local memory. To ensure the greatest computational savings, the master node keeps track of all integral batches stored on the different slaves. The code can reuse undifferentiated two-electron integrals both in the wave function optimization and in the evaluation of second-, third-, and fourth-order molecular properties. Superlinear scaling is achieved in a series of test examples, with speedups of up to 55 achieved for calculations run on medium-sized molecules on 16 processors with respect to the time used on a single processor.
Bhat, Sheeraz Ahmad; Ahmad, Shabbir
2015-11-01
A combined experimental and theoretical study of the structure, vibrational and electronic spectra of temozolomide molecule, which is largely used in the treatment of brain tumours, is presented. FTIR (4000-400 cm-1) and FT-Raman spectra (4000‒50 cm-1) have been recorded and analysed using anharmonic frequency calculations using VPT2, VSCF and CC-VSCF levels of theory within B3LYP/6-311++G(d,p) framework. Anharmonic methods give accurate frequencies of fundamental modes, overtones as well as Fermi resonances and account for coupling of different modes. The anharmonic frequencies calculated using VPT2 and CC-VSCF methods show better agreement with the experimental data. Harmonic frequencies including solvent effects are also computed using IEF-PCM model. The magnitudes of coupling between pair of modes have been calculated using coupling integral based on 2MR-QFF approximation. Intermolecular interactions are discussed for three possible dimers of temozolomide. UV-Vis spectrum, examined in ethanol solvent, is compared with the calculated spectrum at TD-DFT/6-311++G(d,p) level of theory. The electronic properties, such as excitation energy, frontier molecular orbital energies and the assignments of the absorption bands are also discussed.
Gangarapu, S.; Marcelis, A.T.M.; Zuilhof, H.
2013-01-01
The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum
Gutmann, Torsten; Walaszek, Bernadeta; Yeping, Xu; Wächtler, Maria; del Rosal, Iker; Grünberg, Anna; Poteau, Romuald; Axet, Rosa; Lavigne, Guy; Chaudret, Bruno; Limbach, Hans-Heinrich; Buntkowsky, Gerd
2010-08-25
The (2)H quadrupolar interaction is a sensitive tool for the characterization of deuterium-metal binding states. In the present study, experimental solid-state (2)H MAS NMR techniques are used in the investigations of two ruthenium clusters, D(4)Ru(4)(CO)(12) (1) and D(2)Ru(6)(CO)(18) (2), which serve as model compounds for typical two-fold, three-fold, and octahedral coordination sites on metal surfaces. By line-shape analysis of the (2)H MAS NMR measurements of sample 1, a quadrupolar coupling constant of 67 +/- 1 kHz, an asymmetry parameter of 0.67 +/- 0.1, and an isotropic chemical shift of -17.4 ppm are obtained. In addition to the neutral complex, sample 2 includes two ionic clusters, identified as anionic [DRu(6)(CO)(18)](-) (2(-)) and cationic [D(3)Ru(6)(CO)(18)](+) (2(+)). By virtue of the very weak quadrupolar interaction (Quantum chemical DFT calculations at different model structures for these ruthenium clusters were arranged in order to help in the interpretation of the experimental results. It is shown that the (2)H nuclear quadrupolar interaction is a sensitive tool for distinguishing the binding state of the deuterons to the transition metal. Combining the data from the polynuclear complexes with the data from mononuclear complexes, a molecular ruler for quadrupolar interactions is created. This ruler now permits the solid-state NMR spectroscopic characterization of deuterium adsorbed on the surfaces of catalytically active metal nanoparticles.
Simulation of the f-d transitions of lanthanide ions in YPO4 using quantum-chemical calculations
Institute of Scientific and Technical Information of China (English)
Hu Liu-Sen; Wen Jun; Yin Min; Xia Shang-Da
2012-01-01
We constructed an effective one-electron Hamiltonian by using the 4f/5d energies and eigenvectors obtained from the first-principles calculation with the relativistic self-consistent discrete variational Slater software package (DV-Xα).From the effective Hamiltonian,we obtained the crystal-field and spin-orbit interaction parameters for the 4f and 5d electrons of lanthanide ions (Ce3+,Pr3+,Nd3+ and Eu3+) doped in YPO4,and these parameters were used to calculate the 4fN-4fN-15d transition.Comparison with experiments shows that the obtained parameters are reasonable and the excitation spectra can be well predicted.
Musa, Ahmed Y.; Kadhum, Abdul Amir H.; Mohamad, Abu Bakar; Rahoma, Abdalhamid Ahmad B.; Mesmari, Hussein
2010-04-01
The inhibition ability of 4,4-dimethyloxazolidine-2-thione (DMT) for mild steel corrosion in a 1 M HCl solution at 30 °C was studied by means of potentiodynamic polarization, electrochemical impedance spectroscopy (EIS) technique, and scanning electron microscopy (SEM). Quantum chemical calculation based on PM3 method was performed on DMT. The molecule structural parameters, such as the frontier molecular orbital energy HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital), the charge distribution and the fraction of electrons (Δ N) transfer from inhibitor to mild steel were calculated and discussed. Results showed that DMT performed as good inhibiting effect for the corrosion of mild steel in a 1 M HCl solution and inhibition efficiency is higher than 82% at 4 × 10 -3 M DMT. Results indicate that the inhibition efficiencies increased with the concentration of DMT and the area containing S atom is most possible site for bonding the mild steel surface by donating electrons to the metal. Adsorption of the inhibitor on the mild steel surface followed Langmuir adsorption isotherm and the value of the free energy of adsorption Δ G○ads indicated that the adsorption of DMT molecule was a spontaneous process and was typical of chemisorptions.
Dubnikova, Faina; Tamburu, Carmen; Lifshitz, Assa
2016-09-29
The isomerization of o-quinolyl ↔ o-isoquinolyl radicals and their thermal decomposition were studied by quantum chemical methods, where potential energy surfaces of the reaction channels and their kinetics rate parameters were determined. A detailed kinetics scheme containing 40 elementary steps was constructed. Computer simulations were carried out to determine the isomerization mechanism and the distribution of reaction products in the decomposition. The calculated mole percent of the stable products was compared to the experimental values that were obtained in this laboratory in the past, using the single pulse shock tube. The agreement between the experimental and the calculated mole percents was very good. A map of the figures containing the mole percent's of eight stable products of the decomposition plotted vs T are presented. The fast isomerization of o-quinolyl → o-isoquinolyl radicals via the intermediate indene imine radical and the attainment of fast equilibrium between these two radicals is the reason for the identical product distribution regardless whether the reactant radical is o-quinolyl or o-isoquinolyl. Three of the main decomposition products of o-quinolyl radical, are those containing the benzene ring, namely, phenyl, benzonitrile, and phenylacetylene radicals. They undergo further decomposition mainly at high temperatures via two types of reactions: (1) Opening of the benzene ring in the radicals, followed by splitting into fragments. (2) Dissociative attachment of benzonitrile and phenyl acetylene by hydrogen atoms to form hydrogen cyanide and acetylene.
Indian Academy of Sciences (India)
ALEXANDER M ANDRIANOV; IVAN A KASHYN; VIKTOR M ANDRIANOV; MAKSIM B SHUNDALAU; ANTON V HLINISTY; SERGEY V GAPONENKO; ELENA V SHABUNYA -KLYACHKOVSKAYA; ANNA MATSUKOVICH; ABDUL-MALEK S AL- TAMIMI; ALI A EL- EMAM
2016-12-01
The molecular dynamics simulations of the structure of the N'-(adamantan-2-ylidene)benzohydrazide followed by the quantum chemical calculations at the DFT level of theory have identified four stable conformers of this potential antibacterial agent in solution: one “central” cis- and three (“central”, “left” and “right”) trans-conformers. The UV-Vis absorption spectrum in the 220–320 nm region in the ethanol solution reveals two bands that can be primarily explained based on the ab initio calculations of the spectral characteristics of the “side” trans-conformers at the MRPT level of theory. However, the close energy values for thecalculated cis- S₁ ← S₀ and “side” trans- S₂ ← S₀ transitions cannot exclude the presence of cis-conformer in solution. Therefore, the data obtained show that the coexistence of both trans-conformers and cis-conformer should be taken into consideration when studying the pharmaceutical properties of the title molecule.
Kaindl, Reinhard; Sohr, Gerhard; Huppertz, Hubert
2013-12-01
The two oxoborates β-ZnB4O7 and β-CaB4O7 were synthesized and investigated by FTIR- and Raman spectroscopy and ab initio quantum chemical calculations. Maximum and mean deviations between experimentally determined bands and calculated modes ranged between 15-36 cm(-1) and 5-7 cm(-1), respectively, allowing band assignments to vibrational modes in most cases. The complex network structures with tetrahedral BO4 and planar OB3 groups are mirrored by the spectra and numerous vibrational modes, not assignable by standard borates classification schemes. It was confirmed that OB3 units, despite similar force constants and geometry, do not absorb in the same range as BO3 units. Bands in the high wavenumber range are rather caused by B-O-(Zn/Ca), O-B-O, B-O-B, and B-O stretching and bending vibrations. The experimental observation of inactive or Raman-active modes in the absorption spectra indicates defects or structural distortions in both compounds.
DEFF Research Database (Denmark)
Manohara, S.R.; Kumar, V. Udaya; Shivakumaraiah;
2013-01-01
Using the theory of solvatochromism, the difference in the excited-state (μe) and ground-state (μg) dipole moments was determined from Lippert–Mataga, Bakhshiev, Kawski–Chamma–Viallet, and McRae equations for three 1,2-diazines (pyrrolo-pyridazine derivatives). All of these equations are based...... on the variation of Stokes shift with solvent's relative permittivity and refractive index. Further, the change in dipole moment value (Δμ) was also calculated using the variation of Stokes shift with the molecular-microscopic empirical solvent polarity parameter. Theoretical μg values were evaluated by quantum...... chemical calculations using the DFT method by adopting B3LYP/6-31G* level of theory (Gaussian 03) and using the AM1 method (Chem3D Ultra 8.0). It was observed that, dipole moments of diazines in the excited-state (μe) were greater than the corresponding ground-state values (μg), indicating a substantial...
Alver, Özgür; Dikmen, Gökhan
2016-03-01
Possible stable conformers, geometrical molecular structures, vibrational properties as well as band assignments, nuclear magnetic shielding tensors of 2-Fluoro-3-Methylpyridine-5-Boronic Acid (2F3MP5BA) were studied experimentally and theoretically using FT-IR, Raman, (CP/MAS) NMR and XRD spectroscopic methods. FT-IR and Raman spectra were evaluated in the region of 3500-400 cm-1, and 3200-400 cm-1, respectively. The optimized geometric structures, vibrational wavenumbers and nuclear magnetic shielding tensors were examined using Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. 1H, 13C NMR chemical shifts were calculated using the gauge invariant atomic orbital (GIAO) method. 1H, 13C, APT and HETCOR NMR experiments of title molecule were carried out in DMSO solution. 13C CP/MAS NMR measurement was done with 4 mm zirconium rotor and glycine was used as an external standard. Single crystal of 2F3MP5BA was also prepared for XRD measurements. Assignments of vibrational wavenumbers were also strengthened by calculating the total energy distribution (TED) values using scaled quantum mechanical (SQM) method.
Vinod, K. S.; Periandy, S.; Govindarajan, M.
2016-07-01
The spectroscopic and molecular modeling (MM) study includes, FT-IR, FT-Raman and 13C NMR and 1H NMR spectra of the Benzene sulfonamide were recorded for the analysis. The observed experimental and theoretical frequencies (IR and Raman) were assigned according to their distinctive region. The present study of this title molecule have been carried out by hybrid computational calculations of HF and DFT (B3LYP) methods with 6-311+G(d,p) and 6-311++G(d,p) basis sets and the corresponding results are tabulated. The structural modifications of the compound due to the substitutions of NH2 and SO2 were investigated. The minimum energy conformers of the compound were studied using conformational analysis. The alternations of the vibrational pattern of the base structure related to the substitutions were analyzed. The thermodynamic parameters (such as zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment) of Benzene sulfonamide have been calculated. The donor acceptor interactions of the compound and the corresponding UV transitions are found out using NBO analysis. The NMR spectra were simulated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts related to TMS were compared. A quantum computational study on the electronic and optical properties absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The energy gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand group. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase and
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.
Karabacak, Mehmet; Bilgili, Sibel; Atac, Ahmet
2015-11-05
In this work, infrared, Raman and UV spectra of 3,3'-diaminobenzidine (3,3-DAB) were carried out by using density functional theory (DFT)/B3LYP method with 6-311G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the region 4000-400 and 4000-50 cm(-1), respectively. The geometrical parameters, energies and wavenumbers were obtained and fundamental vibrations were assigned on the basis of the potential energy distribution (PED) of the vibrational modes. The UV spectrum of the investigated compound was recorded in the range of 200-400 nm in ethanol and water solutions. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. Thermodynamic properties, Mulliken atomic charges and molecular electrostatic potential (MEP) were calculated for the title molecule. Also the nonlinear optical properties of 3,3-DAB molecule were explored theoretically. As a result, the calculated results were compared with the observed values and generally found to be in good agreement.
Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han
2013-04-02
The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Xu, Li-Hong; Reid, Elias M.; Guislain, Bradley; Hougen, Jon T.; Alekseev, E. A.; Krapivin, Igor
2017-06-01
Hyperfine splittings in methanol have been revisited in three recent publications. (i) Coudert et al. [JCP 143 (2015) 044304] published an analysis of splittings observed in the low-J range. They calculated 32 spin-rotation, 32 spin-spin, and 16 spin-torsion hyperfine constants using the ACES2 package. Three of these constants were adjusted to fit hyperfine patterns for 12 transitions. (ii) Three present authors and collaborators [JCP 145 (2016) 024307] analyzed medium to high-J experimental Lamb-dip measurements in methanol and presented a theoretical spin-rotation explanation that was based on torsionally mediated spin-rotation hyperfine operators. These contain, in addition to the usual nuclear spin and overall rotational operators, factors in the torsional angle α of the form {e^{plusmn;{inα}}}. Such operators have non-zero matrix elements between the two components of a torsion-rotation ^{tr}E state, but have zero matrix elements within a ^{tr}A state. More than 55 hyperfine splittings were successfully fitted using three parameters and the fitted values agree well with ab initio values obtained in (i). (iii) Lankhaar et al. [JCP 145 (2016) 244301] published a reanalysis of the data set from (i), using CFOUR recalculated hyperfine constants based on their rederivation of the relevant expressions. They explain why their choice of fixed and floated parameters leads to numerical values for all parameters that seem to be more physical than those in (i). The results in (ii) raise the question of whether large torsionally-mediated spin-rotation splittings will occur in other methyl-rotor-containing molecules. This abstract presents ab initio calculations of torsionally mediated hyperfine splittings in the E states of acetaldehyde using the same three operators as in (ii) and spin-rotation constants computed by Gaussian09. We explored the first 13 K states for J from 10 to 40 and ν_{t} = 0, 1, and 2. Our calculations indicate that hyperfine splittings in CH_{3}CHO
Saleh, Nidal; Roisnel, Thierry; Guy, Laure; Bast, Radovan; Saue, Trond; Darquié, Benoît; Crassous, Jeanne
2015-01-01
With their rich electronic, vibrational, rotational and hyperfine structure, molecular systems have the potential to play a decisive role in precision tests of fundamental physics. For example, electroweak nuclear interactions should cause small energy differences between the two enantiomers of chiral molecules, a signature of parity symmetry breaking. Enantioenriched oxorhenium(VII) complexes S-(-)- and R-(+)-3 bearing a chiral 2-methyl-1-thio-propanol ligand have been prepared as potential candidates for probing molecular parity violation effects via high resolution laser spectroscopy of the Re=O stretching. Although the rhenium atom is not a stereogenic centre in itself, experimental vibrational circular dichroism (VCD) spectra revealed a surrounding chiral environment, evidenced by the Re=O bond stretching mode signal. The calculated VCD spectrum of the R enantiomer confirmed the position of the sulfur atom cis to the methyl, as observed in the solid-state X-ray crystallographic structure, and showed the ...
Directory of Open Access Journals (Sweden)
Svetlana Begel
2013-06-01
Full Text Available The selectivity of the cryptands [2.2.bpy] and [2.bpy.bpy] for the endohedral complexation of alkali, alkaline-earth and earth metal ions was predicted on the basis of the DFT (B3LYP/LANL2DZp calculated structures and complex-formation energies. The cavity size in both cryptands lay between that for [2.2.2] and [bpy.bpy.bpy], such that the complexation of K+, Sr2+ and Tl3+ is most favorable. While the [2.2.bpy] is moderately larger, preferring Rb+ complexation and demonstrating equal priority for Sr2+ and Ba2+, the slightly smaller [2.bpy.bpy] yields more stable cryptates with Na+ and Ca2+. Although the CH2-units containing molecular bars fixed at the bridgehead nitrogen atoms determine the flexibility of the cryptands, the twist angles associated with the bipyridine and glycol building blocks also contribute considerably.
Naumov, Sergej; von Sonntag, Clemens
2011-11-01
Free radicals are common intermediates in the chemistry of ozone in aqueous solution. Their reactions with ozone have been probed by calculating the standard Gibbs free energies of such reactions using density functional theory (Jaguar 7.6 program). O(2) reacts fast and irreversibly only with simple carbon-centered radicals. In contrast, ozone also reacts irreversibly with conjugated carbon-centered radicals such as bisallylic (hydroxycylohexadienyl) radicals, with conjugated carbon/oxygen-centered radicals such as phenoxyl radicals, and even with nitrogen- oxygen-, sulfur-, and halogen-centered radicals. In these reactions, further ozone-reactive radicals are generated. Chain reactions may destroy ozone without giving rise to products other than O(2). This may be of importance when ozonation is used in pollution control, and reactions of free radicals with ozone have to be taken into account in modeling such processes.
Neeman, Elias M.; Dréan, Pascal; Huet, T. R.
2016-06-01
The emission of volatile organic compounds, from plants has strong revelance for plant physiology, plant ecology and atmospheric chemistry. Camphene (C10H16) is a bicyclic monoterpene which is emitted in the atmosphere by biogenic sources. The structure of the unique stable conformer was optimized using density functional theory and ab initio calculations. The rotational spectrum of camphene was recorded in a supersonic jet expansion with a Fourier transform microwave spectrometer over the range 2-20 GHz. Signals from the parent species and from the ten 13C isotopomers were observed in natural abundance. The rotational and centrifugal distortion parameters were fitted to a Watson's Hamiltonian in the A-reduction. A magnetic hyperfine structure associated with the pairs of hydrogen nuclei in the methylene groups was observed and modeled.The rotational constants coupled to the equilibrium structure calculations were used to determine the r_0 and the r_m(1) gas-phase geometries of the carbon skeleton. The present work provides the first spectroscopic characterization of camphene in the gas phase and these results are also relevant for ozonolysis kinetics study through Criegee intermediates. R. Baraldi, F. Rapparini, O. Facini, D. Spano and P. Duce, Journal of Mediterranean Ecology, Vol.6, No.1, (2005). A. Bracho-Nunez, N. M. Knothe, S. Welter, M. Staudt, W. R. Costa, M. A. R. Liberato, M. T. F. Piedade, and J. Kesselmeier Biogeosciences, 10, 5855-5873, (2013). Minna Kivimäenpää, Narantsetseg Magsarjav, Rajendra Ghimire, Juha-Matti Markkanen, Juha Heijari, Martti Vuorinen and Jarmo K. Holopainen, Atmospheric Environment, 60, 477-485, (2012). R.C. de M. Oliveira and G. F. Bauerfeldt, J. Phys. Chem. A, 119 2802-2812 (2015)
Georgiev, Anton; Bubev, Emil; Dimov, Deyan; Yancheva, Denitsa; Zhivkov, Ivaylo; Krajčovič, Jozef; Vala, Martin; Weiter, Martin; Machkova, Maria
2017-03-01
In this paper three different "push-pull" 4-aminoazobenzene dyes have been synthesized in order to characterize their photochromic behavior in different solvents. The molecular geometry was optimized by DFT/B3LYP functional combined with the standard 6-31 + G(d,p) basis set for trans (E) and cis (Z) isomers and the energy levels of HOMO and LUMO frontier orbitals were computed using IEFPCM solvation in CHCl3 and DMF. The calculated results were compared to the experimental optical band gap and HOMO values of cyclic voltammetry. The intramolecular six-membered hydrogen bond was formed in both isomers of the synthesized dyes. The thermodynamic parameters such as total electronic energy E (RB3LYP), enthalpy H298 (sum of electronic and thermal enthalpies), free Gibbs energy G298 (sum of electronic and thermal free Gibbs energies) and dipole moment μ were computed for trans (E) and cis (Z) isomers in order to estimate the ΔEtrans → cis, Δμtrans → cis, ΔHtrans → cis, ΔGtrans → cis and ΔStrans → cis values. The NBO analysis was performed in order to understand the intramolecular charge transfer and energy of resonance stabilization. The solvatochromic shift was evaluated by UV-VIS spectroscopy in CHCl3 (nonpolar), EtOH (polar protic) and DMF (polar aprotic) solvents to determine the electron withdrawing and donating properties of the substituents on electron transitions energy. Through the increasing solvent polarity a strong bathochromic shift is observed. The photoisomerization experiments have been performed in two solvents CHCl3 (nonpolar) and DMF (polar aprotic) by UV light irradiation with λ = 365 nm at equal concentrations and time of illuminations. The electronic spectra were computed by TD-DFT after geometry optimization using IEFPCM solvation in CHCl3 and DMF. The degree of photoisomerization was calculated for the three azo chromophores in both solvents. By using first derivative of the UV-VIS spectra it was possible to resolve the overlapped
Directory of Open Access Journals (Sweden)
S. Suresh
2016-01-01
Full Text Available The molecular structure of the three compounds Aceclofenac (I, Salicylic Acid (II, and Piroxicam (III has been determined using Gaussian 03W program with B3LYP method using 6-311++G (d,p basis set calculations. The molecular structures were fully optimized with atomic numbering scheme adopted in the study. To understand the mode of binding and molecular interaction, the docking studies of compounds Aceclofenac (I, Salicylic Acid (II, and Piroxicam (III have been carried out with prostaglandin H2 synthase-1 (1PGE as target using induced fit docking. The molecular docking results show that the interactions and energy for Aceclofenac, Salicylic Acid, and Piroxicam show the best results when docked with prostaglandin H2 synthase-1 (1PGE. The hydrogen bonding interactions of compound I (Aceclofenac are prominent with Arginine moiety, those of compound II (Salicylic Acid are prominent with Tyrosine and Serine moieties, and compound III (Piroxicam shows such interaction with Tyrosine and Arginine moieties. These interactions of prostaglandin H2 synthase-1 (1PGE with substrates are responsible for governing COX-1 inhibitor potency which in turn is a direct measure of the potency of the drug.
Lifshitz, Assa; Tamburu, Carmen; Dubnikova, Faina
2009-10-01
The reactions of 1-naphthyl radicals with acetylene were studied behind reflected shock waves in a single-pulse shock tube, covering the temperature range 950-1200 K at overall densities behind the reflected shocks of approximately 2.5 x 10(-5) mol/cm3. 1-Iodonaphthalene served as the source for 1-naphthyl radicals. The [acetylene]/[1-iodonaphthalene] ratio in all of the experiments was approximately 100 to channel the free radicals into reactions with acetylene rather than iodonaphthalene. Only two major products resulting from the reactions of 1-naphthyl radicals with acetylene and with hydrogen atoms were found in the post shock samples. They were acenaphthylene and naphthalene. Some low molecular weight aliphatic products at rather low concentrations, resulting from an attack of various free radicals on acetylene, were also found in the shocked samples. In view of the relatively low temperatures employed in the present experiments, the unimolecular decomposition rate of acetylene is negligible. One potential energy surface describes the production of acenaphthylene and 1-naphthyl acetylene, although the latter was not found experimentally due to the high barrier (calculated) required for its production. Using quantum chemical methods, the rate constants for three unimolecular elementary steps on the surface were calculated using transition state theory. A kinetics scheme containing 16 elementary steps was constructed, and computer modeling was performed. An excellent agreement between the experimental yields of the two major products and the calculated yields was obtained. Differences and similarities in the potential energy surfaces of 1-naphthyl radical + acetylene and those of ethylene are presented, and the kinetics mechanisms are discussed.
Soliman, Saied M.; Albering, Jörg; Abu-Youssef, Morsy A. M.
2017-07-01
The reaction between nitric acid and pyridine-4-carboxaldoxime (P4A) afford the corresponding pyridinum nitrate salt (P4AN). Its X-ray structure is measured and compared with the related P4A salts. The DFT/B3LYP results showed that both the P4A and P4AN favored the Syn-I form which has the lowest energy among the other possible isomers. Transition state calculations predicted that the Syn-I form is the thermodynamically and kinetically most stable form. The X-ray solid state structure of the new nitrate salt (P4AN) indicated that the labile proton favored the N-atom of the pyridine ring. DFT studies showed that the same is true for its solution in polar solvents. In contrast, the pyridinium cation is not favored either in the gas phase or solution of P4AN in nonpolar solvent. In these cases, the proton favored to bond with one O-atom from the nitrate group. Second order interaction energies and Mayer bond order values revealed these results. The bond order of the Nsbnd H bond is higher in polar solvents as well as at the experimental structure than either in the gas phase or non polar solvents. The topology parameters obtained from the atoms in molecules (AIM) analysis were used to describe the nature of the Nsbnd H and Osbnd H bonds. The bond critical points (BCP) were found to be close to the H-atoms in case of stronger interaction.
Indian Academy of Sciences (India)
Anuradha Sankaran; E J Padma Malar; Venkatapuram Ramanujam Vijayaraghavan
2015-07-01
Cu(II) ion catalyzed kinetics of oxidation of H2O2 by [NiIIIL2] (L2 = 1,8-bis(2-hydroxyethyl)-1,3,6,8,10,13-hexaazacyclotetradecane) was studied in aqueous acidic medium in the presence of sulphate ion. The rate of oxidation of H2O2 by [NiIIIL2] is faster than that by [NiIIIL1] (L1 = 1,4,8,11-tetraazacyclote-tradecane) in sulphate medium. DFT calculations at BP86/def2-TZVP level lead to different modes of bonding between [NiL]II/III and water ligands (L = L1 and L2). In aqueous medium, two water molecules interact with [NiL]II through weak hydrogen bonds with L and are tilted by ∼23° from the vertical axis forming the dihydrate [NiL]2+.2H2O. However, there is coordinate bond formation between [NiL1]III and two water molecules in aqueous medium and an aqua and a sulphato ligand in sulphate medium leading to the octahedral complexes [NiL1(H2O)2]3+ and [NiL1(SO4)(H2O)]+. In the analogous [NiL2]III, the water molecules are bound by hydrogen bonds resulting in [NiL2]3+.2H2O and [NiL2(SO4)]+.H2O. As the sulphato complex [NiL2(SO4)]+.H2O is less stable than [NiL1(SO4)(H2O)]+ in view of the weak H-bonding interactions in the former it can react faster. Thus the difference in the mode of bonding between Ni(III) and the water ligand can explain the rate of oxidation of H2O2 by [NiIIIL] complexes.
Energy Technology Data Exchange (ETDEWEB)
Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J. [Madrid Institute for Advanced Studies, IMDEA Nanoscience, Calle Faraday 9, Campus Cantoblanco, 28049 Madrid (Spain); Beljonne, D. [Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc 20, 7000 Mons (Belgium)
2015-09-21
Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.
Wetmore, Stacey D.; Eriksson, Leif A.; Boyd, Russell J.
1998-12-01
The hyperfine coupling constants (HFCCs) in the hydroxyl radical are investigated through comparison of results obtained from a variety of quantum chemical methods. The couplings obtained from the multi-reference configuration interaction (MRCI) wave function, built upon the restricted open-shell Hartree-Fock (ROHF) reference determinant, are investigated in terms of the basis set, the configuration selection energy threshold, and the size of the reference space. Overall results which converge to the experimental couplings are obtained for hydrogen, but not for oxygen. In particular, the MRCI method shows no improvement over density functional theory (the B3LYP functional), for the calculation of Aiso(17O). On the other hand, results in excellent agreement with experiment are obtained through the use of the quadratic configuration interaction (QCISD) method based on the unrestricted HF (UHF) reference determinant with the identical basis sets. Examination of UHF and ROHF based coupled-cluster methods, CCSD and CCSD(T), indicates that once a high enough level of electron correlation is included, the oxygen HFCC is independent of the form of the reference determinant. Unlike the ROHF-CCSD method, which yields reliable results once the effects of triple excitations have been taken into account, the MRCI wave function cannot easily be adjusted to account for the inadequacies of the ROHF reference determinant in order to accurately predict 17O HFCCs.
van der Tak, Floris; Harding, Michael; Gauss, Jürgen
2009-01-01
We have observed the rotational ground-state (J = 1-0) transitions of DCO+, HN13C and DNC with the IRAM 30m telescope toward the dark cloud LDN 1512 which has exceptionally narrow lines permitting hyperfine splitting to be resolved in part. The measured splittings of 50-300 kHz are used to derive nuclear quadrupole and spin-rotation parameters for these species. The measurements are supplemented by high-level quantum-chemical calculations using coupled-cluster techniques and large atomic-orbital basis sets. We find eQq = +151.12 (400) kHz and C_I = -1.12 (43) kHz for DCO+, eQq = 272.5 (51) kHz for HN13C, and eQq(D) = 265.9 (83) kHz and eQq(N) = 288.2 (71) kHz for DNC. The numbers for DNC are consistent with previous laboratory data, while our constants for DCO+ are somewhat smaller than previous results based on astronomical data. For both DCO+ and DNC, our results are more accurate than previous determinations. Our results are in good agreement with the corresponding best theoretical estimates. We also deriv...
Belyakov, Alexander V.; Sigolaev, Yrii F.; Shlykov, Sergey A.; Wallevik, Sunna Ó.; Jonsdottir, Nanna R.; Jonsdottir, Sigridur; Kvaran, Ágúst; Bjornsson, Ragnar; Arnason, Ingvar
2017-03-01
The conformational preference of the cyano group of the 1-cyano-1-silacyclohexane was studied experimentally by means of gas electron diffraction (GED) and dynamic nuclear magnetic resonance (DNMR) as well as by quantum chemical (QC) calculations applying high-level coupled cluster methods as well as DFT methods. According to the GED experiment, the compound exists in the gas-phase as a mixture of two conformers possessing the chair conformation of the six-membered ring and Cs symmetry while differing in the axial or equatorial position of the substituent (axial = 84(12) mol %/equatorial = 16(12) mol %) at T = 279(3) K, corresponding to an A value (Gax - Geq) of -1.0(4) kcal mol-1. Gas-phase CCSD(T) calculations predict an A value of -0.72 kcal mol-1 at 279 K. In contrast, the low-temperature 13C NMR experiments resulted in an axial/equatorial ratio of 35/65 mol % at 120 K corresponding to an A value of 0.14 kcal mol-1. An average value for ΔG#e→a = 5.6 ± 0.1 kcal mol-1 was obtained for the temperature range 110-145 K. The dramatically different conformational behaviour in the gas-phase (GED) compared to the liquid phase (DNMR) suggests a strong solvation effect. According to natural bond orbital analysis the axial conformer of the title compound is an example of stabilization of a form, which is not favored by electrostatic effects and is favored predominantly by steric and conjugation effects.
Sun, Yuzhen; Pan, Wenxiao; Lin, Yuan; Fu, Jianjie; Zhang, Aiqian
2016-01-01
Short-chain chlorinated paraffins (SCCPs) are still controversial candidates for inclusion in the Stockholm Convention. The inherent mixture nature of SCCPs makes it rather difficult to explore their environmental behaviors. A virtual molecule library of 42,720 C10-SCCP congeners covering the full structure spectrum was constructed. We explored the structural effects on the thermodynamic parameters and environmental degradability of C10-SCCPs through semi-empirical quantum chemical calculations. The thermodynamic properties were acquired using the AM1 method, and frontier molecular orbital analysis was carried out to obtain the E(HOMO), E(LUMO) and E(LUMO)-E(HOMO) for degradability exploration at the same level. The influence of the chlorination degree (N(Cl)) on the relative stability and environmental degradation was elucidated. A novel structural descriptor, μ, was proposed to measure the dispersion of the chlorine atoms within a molecule. There were significant correlations between thermodynamic values and N(Cl), while the reported N(Cl)-dependent pollution profile of C10-SCCPs in environmental samples was basically consistent with the predicted order of formation stability of C10-SCCP congeners. In addition, isomers with large μ showed higher relative stability than those with small μ. This could be further verified by the relationship between μ and the reactivity of nucleophilic substitution and OH attack respectively. The C10-SCCP congeners with less Cl substitution and lower dispersion degree are susceptible to environmental degradation via nucleophilic substitution and hydroxyl radical attack, while direct photolysis of C10-SCCP congeners cannot readily occur due to the large E(LUMO)-E(HOMO) values. The chlorination effect and the conclusions were further checked with appropriate density functional theory (DFT) calculations.
Energy Technology Data Exchange (ETDEWEB)
Vent-Schmidt, Thomas
2015-11-30
During this thesis, the matrix-isolation technique in conjuction with quantum-chemical calculations has been employed in order to synthesize and characterize new compounds. The focus of the study were new species of the actinide and lanthanide series, but the photochemistry of XeO{sub 4} and the polyfluorides were also investigated. Based on the experience of laser ablated uranium and thorium atoms with H{sub 2} and F{sub 2} the reaction of these actinide atoms with HF has been investigated. The main products in these experiments are HThF and HUF which contain an actinide metal in the rather scarce +II oxidation state. In addition, the deuterated compounds have also been prepared and the isotopic shifts support the assignment. The higher hydride fluorides of thorium such as HThF{sub 3}, H{sub 2}ThF{sub 2} and H{sub 3}ThF have also been observed, whereas there is only little evidence for higher uranium hydride fluorides. The different behavior of the two metals under similar reaction conditions has been investigated theoretically. Besides the hydride fluorides, the reaction of the actinide atoms with HF gives also rise to the low valent fluorides and hydrides such as AnH and AnF (An = U, Th). These compounds have already been identified in experiments using fluorine or hydrogen as reagent, but a more reliable assignment can be made in these experiments due to the lower concentration of H or F. In addition, ThF{sub 2} has been observed in these experiments and there is evidence for the unknown difluoride of uranium, which will be addressed in a future paper. Experiments with laser ablated uranium and thorium atoms were extended to the reaction of these metals with H{sub 2}Se. Previous experiments using H{sub 2}O and H{sub 2}S instead of H{sub 2}Se yielded H{sub 2}AnX (An = U, Th; X = O, S) compounds which show evidence for an actinide-chalcogenide multiple bond. The new synthesized species H{sub 2}ThSe and H{sub 2}USe are characterized by their symmetric and
Quantum Entanglement and Chemical Reactivity.
Molina-Espíritu, M; Esquivel, R O; López-Rosa, S; Dehesa, J S
2015-11-10
The water molecule and a hydrogenic abstraction reaction are used to explore in detail some quantum entanglement features of chemical interest. We illustrate that the energetic and quantum-information approaches are necessary for a full understanding of both the geometry of the quantum probability density of molecular systems and the evolution of a chemical reaction. The energy and entanglement hypersurfaces and contour maps of these two models show different phenomena. The energy ones reveal the well-known stable geometry of the models, whereas the entanglement ones grasp the chemical capability to transform from one state system to a new one. In the water molecule the chemical reactivity is witnessed through quantum entanglement as a local minimum indicating the bond cleavage in the dissociation process of the molecule. Finally, quantum entanglement is also useful as a chemical reactivity descriptor by detecting the transition state along the intrinsic reaction path in the hypersurface of the hydrogenic abstraction reaction corresponding to a maximally entangled state.
Morisawa, Yusuke; Tachibana, Shin; Ehara, Masahiro; Ozaki, Yukihiro
2012-12-01
Attenuated total reflection far-ultraviolet (ATR-FUV) spectra containing Rydberg states of n-alkanes (C(m)H(2m+2); m varies in the range 5-9) and branched alkanes observed in the liquid phase were investigated by quantum chemical calculations with the aim of elucidating electronic transitions from σ orbitals of liquid n- and branched alkanes. New assignments are proposed based on the time-dependent density functional theory (TD-DFT) and symmetry-adapted cluster configuration interaction (SAC-CI) calculations, and the differences in these spectra are analyzed in detail. The FUV spectra of n-alkanes show a broad asymmetric feature near 8.3 eV. The strong band at ∼8.3 eV shows a red shift with a significant increase in intensity as the carbon chain length increases, which is attributed to the overlapping transitions from the third (or fourth) highest occupied molecular orbitals HOMO-2 (or HOMO-3) and HOMO-1 to Rydberg 3p(y) by the TD-DFT and SAC-CI calculations. This band was previously assigned to the overlap of two peaks arising from the transition from the HOMO to 3p and from the HOMO-1 to 3s based on their term values. Although the most intense transition, T1, is from HOMO-2 for m = 5 and 6 and HOMO-3 for m varying in the range of 7-9, the shape of Kohn-Sham molecular orbital for T1 is similar among the all-alkanes investigated. The theoretical result also has demonstrated that the red shift originates in both stabilization of the Rydberg 3p(y) and destabilization of the occupied orbitals. The intensity of the shoulder at 7.7 eV drastically increases in the spectra of the branched alkanes, especially for those with quaternary carbon atoms such as 2,2-dimethyl butane. This increase in intensity is caused by a reduction in symmetry in the branched alkanes, which leads the forbidden transitions to Rydberg 3s to allowed transitions. In this way, the present study has provided new insight into the existence of their Rydberg transitions and the shape of the relevant
Quesada-Moreno, María Mar; Avilés-Moreno, Juan Ramón; Márquez-García, A A; López-González, Juan Jesús
2014-06-01
The behavior of L-cysteine (C3H7NO2S, (2R)-2-amino-3-sulfanylpropanoic acid) in water at different pH values was analyzed both experimentally and theoretically. The behavior was studied at pH values of 5.21 (at this pH, L-cysteine is a zwitterionic species), 1.00 (protonated species), 8.84 (monodeprotonated species), and 13.00 (dideprotonated species). We carried out a vibrational study using nonchiroptical (IR-Raman) and chiroptical (VCD) techniques complemented by quantum chemical calculations. We adopted a dual strategy, as follows. (i) The hybrid density functionals B3LYP and M062X and the ab initio MP2 method were employed, with the same 6-311++G (d,p) basis set, in order to characterize the relative energies and structures of an extensive set of conformers of L-cysteine. The presence of water was included by utilizing the IEF-PCM implicit solvation model. (ii) The vibrational analysis was made using a chirality-sensitive using a chirality-sensitive technique (VCD) and chirality-insensitive techniques (IR, including MIR and FIR, and Raman), especially in aqueous solution. The results obtained theoretically and experimentally were compared in order to deduce the most stable structures at each pH. Moreover, for the first time, the monodeprotonated anion of L-cysteine was detected in aqueous solution by means of IR, Raman and vibrational circular dichroism (VCD). Finally, analysis of the low-frequency region using the IR and Raman techniques was shown to be a very important way to understanding the conformational preference of the zwitterionic species.
Bani-Fwaz, Mutasem Z.; Fazary, Ahmed E.; Becker, Gerd
2017-10-01
This work has involved the reaction of kinetically stable 2-tert-buty-lλ3-phospha-alkyne, tBu-Ctbnd P, with dichloro(dialkylamino)arsines, in which the isolated products were characterized by spectroscopic methods; additionally, the results of X-ray structure analyses were confirmed by quantum chemical calculations using Gaussian 98 molecular modeling software. The arsenic component of the starting material is completely lost, probably as a precipitate of insoluble ;arsenic(I) chloride,; and unusual oligocycle 2,4,6-tri-tert-butyl-3-chloro-1-dialkylamino-1λ5σ4,3λ3σ3,5λ3σ2-triphosphabicyclo[2.2.0]hexa-1,5-diene (1) - an ylide with an unusually long P-Cl bond (245.5 p.m.) - could be isolated. From these reactions, compounds 1a to 1d differing by their substituents at nitrogen were isolated as deep red, cuboid-shaped single crystals. X-ray structure analyses reveal molecules which are characterized by an ylidic and a regular P-C double bond of almost equal length [P1⊕-C2⊖av.172.2 p.m., P5-C6av.169.6 p.m.]. In addition to these two characteristic features the average bond length P3-C2 is found to be considerably shortened to a value of 172.7 p.m., whereas the adjacent phosphorus-chlorine bond P3-Cl1 is strongly elongated to 245.5 p.m.
Quantum Monte Carlo Calculations of Light Nuclei
Pieper, Steven C
2007-01-01
During the last 15 years, there has been much progress in defining the nuclear Hamiltonian and applying quantum Monte Carlo methods to the calculation of light nuclei. I describe both aspects of this work and some recent results.
Energy Technology Data Exchange (ETDEWEB)
Welsch, Ralph, E-mail: rwelsch@uni-bielefeld.de; Manthe, Uwe, E-mail: uwe.manthe@uni-bielefeld.de [Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld (Germany)
2014-08-07
The mode-selective chemistry of the title reaction is studied by full-dimensional quantum dynamics simulation on an accurate ab initio potential energy surface for vanishing total angular momentum. Using a rigorous transition state based approach and multi-configurational time-dependent Hartree wave packet propagation, initial state-selected reaction probabilities for many ro-vibrational states of methane are calculated. The theoretical results are compared with experimental trends seen in reactions of methane. An intuitive interpretation of the ro-vibrational control of the chemical reactivity provided by a sudden model based on the quantum transition state concept is discussed.
Directory of Open Access Journals (Sweden)
Simone Di Micco
2013-12-01
Full Text Available In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of 13C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of 13C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.
Quantum-Chemical Ab Initio Calculations on Ala-(C5H5Al) and Galabenzene (C5H5Ga)
Mersmann, Stefanie; Mouhib, Halima; Baldofski, Matthias; Raabe, Gerhard
2014-07-01
Quantum-chemical ab initio and time-dependent density functional theory (TD-DFT) calculations employing various basis sets were used to elucidate the spatial as well as the electronic structure of C5H5Al () and C5H5Ga (2) (ala- and galabenzene). The lowest closed shell singlet states of both compounds were found to have a non-planar structure of CS symmetry with C-X-C bond angles of about 116° (MP2/6-311++G**) and 125° (CCSD/aug-cc-pVDZ). At approximately 103°, the corresponding angles of the lowest triplets are significantly smaller. The lowest triplet state of alabenzene is also non-planar (CS) at the MP2 level while optimization with the CCSD and the CASPT2 method resulted in planar structures with C2v symmetry. The corresponding state of galabenzene has C2v symmetry at all levels of optimization. The relative stability of the lowest closed shell singlet and the lowest triplet (ΔE(T1-S0)) state is small and its sign even strongly method-dependent. However, according to the highest levels of theory applied in this study the singlet states of both molecules are slightly lower in energy than the corresponding triplets with singlet/triplet gaps between about 0.5 and 5.8 kcal/mol in favour of the singlet states. Most of the applied methods give a slightly smaller splitting for ala- than for galabenzene. Independent of the applied method (TD-DFT/CAM-B3LYP/6-311++G(3df,3pd)//MP2/6- 311++G** or SAC-CI/6-31++G(3df,3pd)//MP2/6-311++G**), the general shape of the calculated UV/VIS spectral curves are quite similar for the lowest singlet states of ala- and galabenzene, and the same applies to the spectra of the normal modes. The calculated UV/VIS spectra of C5H5Al and C5H5Ga are featured by long wavelength bands of moderate intensity around 900 nm at the TD-DFT and between 1300 and 1500 nm at the SAC-CI level. According to both methods these bands are predominantly due to HOMO(π)→LUMO(σ*) transitions. The results of isodesmic bond separation reactions for the
van der Tak, F. F. S.; Müller, H. S. P.; Harding, M. E.; Gauss, J.
2009-11-01
Context: Knowledge of the hyperfine structure of molecular lines is useful for estimating reliable column densities from observed emission, and essential for the derivation of kinematic information from line profiles. Aims: Deuterium bearing molecules are especially useful in this regard, because they are good probes of the physical and chemical structure of molecular cloud cores on the verge of star formation. However, the necessary spectroscopic data are often missing, especially for molecules which are too unstable for laboratory study. Methods: We have observed the ground-state (J = 1{-}0) rotational transitions of DCO^+, HN13C and DNC with the IRAM 30 m telescope toward the dark cloud LDN 1512 which has exceptionally narrow lines permitting hyperfine splitting to be resolved in part. The measured splittings of 50-300 kHz are used to derive nuclear quadrupole and spin-rotation parameters for these species. The measurements are supplemented by high-level quantum-chemical calculations using coupled-cluster techniques and large atomic-orbital basis sets. Results: We find eQq = + 151.12 (400) kHz and CI = -1.12 (43) kHz for DCO^+, eQq = 272.5 (51) kHz for HN13C, and eQq(D) =265.9 (83) kHz and eQq(N) = 288.2 (71) kHz for DNC. The numbers for DNC are consistent with previous laboratory data, while our constants for DCO+ are somewhat smaller than previous results based on astronomical data. For both DCO+ and DNC, our results are more accurate than previous determinations. Our results are in good agreement with the corresponding best theoretical estimates, which amount to eQq = 156.0 kHz and CI = -0.69 kHz for DCO^+, eQq = 279.5 kHz for HN13C, and eQq(D) = 257.6 kHz and eQq(N) = 309.6 kHz for DNC. We also derive updated rotational constants for HN13C: B = 43 545.6000 (47) MHz and D = 93.7 (20) kHz. Conclusions: The hyperfine splittings of the DCO^+, DNC and HN13C J = 1{-}0 lines range over 0.47-1.28 km s-1, which is comparable to typical line widths in pre
Quantum-chemical studies on porphyrins, fullerenes and carbon nanostructures
Loboda, Oleksandr
2014-01-01
This book presents theoretical studies of electronic structure, optical and spectroscopic properties of a number of compounds. It presents new, faster calculation methods for applications in quantum-chemical theory of electronic structures.
Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet
2015-04-01
In this work, the molecular conformation, vibrational and electronic analysis of isonicotinic acid N-oxide (iso-NANO) were presented in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. The geometry optimization and energies associated possible two conformers (Rot-I and Rot-II) were computed. The 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 and PQS program. The obtained structures were analyzed with the Atoms in Molecules (AIMs) methodology. The computational results diagnose the most stable conformer of iso-NANO as the Rot-I form. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (OPDOS) diagrams analysis for the most stable conformer (Rot-I) were calculated using the same method. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. As a result, the optimized geometry and calculated spectroscopic data show a good agreement with the experimental results.
Relaxation Method For Calculating Quantum Entanglement
Tucci, R R
2001-01-01
In a previous paper, we showed how entanglement of formation can be defined as a minimum of the quantum conditional mutual information (a.k.a. quantum conditional information transmission). In classical information theory, the Arimoto-Blahut method is one of the preferred methods for calculating extrema of mutual information. We present a new method akin to the Arimoto-Blahut method for calculating entanglement of formation. We also present several examples computed with a computer program called Causa Comun that implements the ideas of this paper.
Hayashi, Tomohiko; Matsuura, Azuma; Sato, Hiroyuki; Sakurai, Minoru
2012-01-01
Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction. PMID:27493528
Energy Technology Data Exchange (ETDEWEB)
Musa, Ahmed Y., E-mail: ahmed.musa@ymail.com [Department of Chemical and Process Engineering, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor (Malaysia); Kadhum, Abdul Amir H.; Mohamad, Abu Bakar; Takriff, Mohd Sobri [Department of Chemical and Process Engineering, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor (Malaysia)
2011-09-15
Highlights: {yields} This work deals with a study of chemical additives for corrosion inhibition of mild steel in acidic conditions. {yields} The effects of the additive 4,4-dimethyl-3-thiosemicarbazide (DTS) on mild steel were studied by means of electrochemical techniques. {yields} Quantum chemical calculations and molecular dynamic model were performed to characterize the inhibition mechanism. {yields} The calculations provided information that helps in the analysis/interpretation of the experimental work. - Abstract: The inhibition of mild steel corrosion in a 2.5 M H{sub 2}SO{sub 4} solution by 4,4-dimethyl-3-thiosemicarbazide (DTS) was studied at 30 deg. C using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS). Quantum chemical parameters were calculated for DTS using PM3-SCF method. The molecular dynamic method was performed to simulate the adsorption of the DTS molecules on Fe surface. Results showed that DTS performed excellent as inhibitor for mild steel corrosion in a 2.5 M H{sub 2}SO{sub 4} solution and indicated that the inhibition efficiencies increase with the concentration of inhibitor. Theoretical results indicated that DTS could adsorb on the mild steel surface firmly through heteroatoms.
Challenges in Large Scale Quantum Mechanical Calculations
Ratcliff, Laura E; Huhs, Georg; Deutsch, Thierry; Masella, Michel; Genovese, Luigi
2016-01-01
During the past decades, quantum mechanical methods have undergone an amazing transition from pioneering investigations of experts into a wide range of practical applications, made by a vast community of researchers. First principles calculations of systems containing up to a few hundred atoms have become a standard in many branches of science. The sizes of the systems which can be simulated have increased even further during recent years, and quantum-mechanical calculations of systems up to many thousands of atoms are nowadays possible. This opens up new appealing possibilities, in particular for interdisciplinary work, bridging together communities of different needs and sensibilities. In this review we will present the current status of this topic, and will also give an outlook on the vast multitude of applications, challenges and opportunities stimulated by electronic structure calculations, making this field an important working tool and bringing together researchers of many different domains.
Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet
2013-11-01
In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400 cm-1 and 3500-50 cm-1, respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The 1H, 13C and HMQC (1H-13C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400 nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.
Demir, Pınar; Akman, Feride
2017-04-01
A newly synthesized polycaprolactone (PCL) and polyurethane (PU) polymers, which grafted onto poly (ethylmethacrylate-co-2-hydroxyethyl methacrylate) (PEMA-co-PHEMA) were characterized both theoretically and experimentally. The FTIR and 1H NMR spectra were recorded for the PCL and PU polymers and the experimental values were compared the theoretical values. The molecular structure evaluation, vibrational frequencies and 1H NMR chemical shift values, which carried out by using gauge including atomic orbital (GIAO) approach, of the PCL and PU polymers were calculated by using density functional method (DFT/B3LYP) with 6-311G (d, p) as a basis set in the ground state. The calculated data such as vibrational frequencies and chemical shift values show good agreement with experimental values. Besides, the thermodynamic properties such as rotational temperatures, rotational constants, zero-point vibrational energy, specific heat capacity, thermal energy, entropy, enthalpy, the electronic properties such as HOMO and LUMO energies, and molecular electrostatic potential (MEP) surfaces for the PCL and PU were calculated and interpreted.
Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José
2011-05-20
A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.
Mathammal, R; Sudha, N; Guru Prasad, L; Ganga, N; Krishnakumar, V
2015-02-25
In this work, the vibrational characteristics of 2-Benzylpyridine have been investigated. The structure of the molecule has been optimized and the structural characteristics of the molecule have been determined by density functional theory B3LYP method with 6-31G(d,p) basis set. The infrared and Raman spectra have been simulated from calculated intensities. Both the experimental and theoretical vibrational data confirms the presence of functional groups in the title compound. The (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital method. UV-Visible spectrum of the title compound was recorded in the region 190-1100 nm and the electronic properties HOMO and LUMO energies were calculated by CIS approach. Nonlinear optical and thermodynamic properties were interpreted. All the calculated results were compared with the available experimental data of the title molecule. Copyright © 2014 Elsevier B.V. All rights reserved.
Gökce, Halil; Bahçeli, Semiha
2013-12-01
In this study, molecular geometries, experimental vibrational wavenumbers, electronic properties and quantum chemical calculations of 2-thiopheneglyoxylic acid molecule, (C6H4O3S), and its metal halides (Cd, Co, Cu, Ni and Zn) which are used as pharmacologic agents have been investigated experimentally by FT-IR, micro-Raman and UV-visible spectroscopies and elemental analysis. Meanwhile the vibrational calculations were verified by DFT/B3LYP method with 6-311++G(d,p) and LANL2DZ basis sets in the ground state, for free TPGA molecule and its metal halide complexes, respectively, for the first time. The calculated fundamental vibrational frequencies for the title compounds are in a good agreement with the experimental data.
Directory of Open Access Journals (Sweden)
Humberto J. Domínguez
2014-01-01
Full Text Available Marine organisms are an increasingly important source of novel metabolites, some of which have already inspired or become new drugs. In addition, many of these molecules show a high degree of novelty from a structural and/or pharmacological point of view. Structure determination is generally achieved by the use of a variety of spectroscopic methods, among which NMR (nuclear magnetic resonance plays a major role and determination of the stereochemical relationships within every new molecule is generally the most challenging part in structural determination. In this communication, we have chosen okadaic acid as a model compound to perform a computational chemistry study to predict 1H and 13C NMR chemical shifts. The effect of two different solvents and conformation on the ability of DFT (density functional theory calculations to predict the correct stereoisomer has been studied.
Sridevi, C; Velraj, G
2014-01-01
This study represents the conformation, tautomeric stability, protonation and deprotonation effects, vibrational, electronic, NBO and NMR aspects of 2,4-Dioxoimidazolidine-5-acetic acid (DOIAA). Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. Tautomerism and the effect of solvent on the tautomeric equilibria in the gas phase and in different solvents were studied. The protonation and deprotonation effects on the reactivity and conformations of DOIAA were investigated. Electronic transitions were also studied and the most prominent transition corresponds to π→π*. Natural bond orbital (NBO) analysis was also carried out to find the intramolecular interactions and their stabilization energy. In DOIAA, the interaction between the lone pair donor orbital (n(LP1N5)) and the acceptor antibonding orbital π*(C6O7) reveals the strong stabilization energy of 224.9 kJ mol(-1). Molecular electrostatic potential (MEP) was calculated to predict the reactive sites of the title compound. The NMR results indicated that the observed chemical shifts for NH, COOH protons of DOIAA not only depend on the structure of the molecule being studied but also on the nature of the solvent, concentration of the sample and the presence of the other exchangeable protons.
Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.
2017-10-01
The synthesis and the X-ray structure of the Zn(II) zwitterionic complex:1-ethylpiperaziniumtrichlorozincate (II) are described. In the atomic arrangement, the ZnCl3N entities, grouped in pairs, are deployed along the b-axis to form layers. The organic entities are inserted between these layers through Nsbnd H⋯Cl and Csbnd H⋯Cl hydrogen bonds to form infinite three-dimensional network. The 3D Hirshfeld surfaces were investigated for intermolecular interactions. The optimized geometry, Mulliken charge distribution, molecular electrostatic potential (MEP) maps and thermodynamic properties have been calculated using the Lee-Yang-Parr correlation functional B3LYP with the LanL2DZ basis set. The HOMO and LUMO energy gap and chemical reactivity parameters were made. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray crystal structure. The vibrational absorption bands were identified by infrared spectroscopy. DFT calculations allowed the attribution of the NMR peaks and of the IR bands.
Sarıkaya, Ebru Karakaş; Bahçeli, Semiha; Varkal, Döndü; Dereli, Ömer
2017-08-01
In this work, the study of the6-chloro-4-hydroxy-3-phenyl pyridazine compound, (C10 H7 N2 O Cl with synonym 4-pyridazinol, 6-chloro-3-phenyl-), was verified experimentally by using the Fourier Transformed Infrared (FT-IR), micro-Raman and UV/vis (in N,N-dimethylformamide solvent) spectroscopies. Furthermore, the optimized molecular geometry, conformatinal analysis, vibrational frequencies, the simulated UV/vis spectra (in gas and in N,N-dimethylformamide solvent), 1H and 13C NMR chemical shift (in gas, in chloroform and N,N-dimethylformamide in solvents) values, HOMO-LUMO analysis, the molecular electrostatic potential (MEP) surface and thermodynamic parameters ofthe6-chloro-4-hydroxy-3-phenyl pyridazine compound were calculated by using DFT/B3LYP method with 6-311++G(d,p) basis set in ground state. The comparison of the calculated and vibrational frequencies with the experimental values provides important information about the title compound.
Gür, Mahmut; Muğlu, Halit; Çavuş, M. Serdar; Güder, Aytaç; Sayıner, Hakan S.; Kandemirli, Fatma
2017-04-01
A series of 1,3,4-thiadiazole derivatives including 2- and 3-methoxy cinnamic acids were synthesized, and their structures were elucidated by the UV, IR, 1H NMR, 13C NMR spectroscopies and elemental analysis. The UV and IR calculations of the molecules were performed by using B3LYP, HF and MP2 methods with selected 6-311++G(2d,2p), 6-311++G(3df,3pd) and cc-pvtz basis sets. Dipole moment, polarizability, chemical hardness/softness and electronegativity were also calculated and analyzed. Experimental FT-IR spectra and UV-Vis spectrum of the compounds were compared with theoretical data. Furthermore, antioxidant activities of the compounds were practised via different test methods such as 2,2-diphenyl-1-picryl-hydrazyl (DPPHrad), N,N-dimethyl-p-phenylenediamine (DMPDrad +), and 2,2‧-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTSrad +) scavenging activity assays. When compared with standards (BHA-Butylated hydroxyanisole, RUT-Rutin, and TRO-Trolox), it was observed that especially XIII and XIV which include methoxy groups at the o- and m-positions, respectively, had effective activities.
Neeman, Elias M.; Aviles Moreno, Juan-Ramon; Huet, T. R.
2016-06-01
Several monoterpenes and terpenoids are biogenic volatile organic compounds which are emitted in the atmosphere, where they react with OH, O_3 and NO_x etc. to give rise to several oxidation and degradation products. Their decomposition products are a major source of secondray organic aerosol (SOA). Spectroscopic information on these atmospheric species is still very scarce. The rotational spectrum of nopinone (C_9H14O) one of the major oxidation products of β-pinene, and of its water complexes were recorded in a supersonic jet expansion with a Fourier transform microwave spectrometer over the range 2-20 GHz. The structure of the unique stable conformer of the nopinone was optimized using density functional theory and ab initio calculations. Signals from the parent species and from the 13C and 18O isotopomers were observed in natural abundance. A magnetic hyperfine structure associated with the pairs of hydrogen nuclei in the methylene groups was observed and modeled. The structures of several conformers of the nopinone-water complexes with up to three molecules of water were optimized using density functional theory and ab initio calculations. The energetically most stable of calculated conformers were observed and anlyzed. The rotational and centrifugal distortion parameters were fitted to a Watson's Hamiltonian in the A-reduction. The present work provides the first spectroscopic characterization of nopinone and its water complexes in the gas phase. A. Calogirou, B.R. Larsen, and D. Kotzias, Atmospheric Environment, 33, 1423-1439, (1999) P. Paasonen et al., Nat. Geosci., 6, 438-442 (2013) D. Zhang and R. Zhang The Journal of Chemical Physics, 122, 114308, (2005) R. Winterhalter et al. Journal of Atmospheric Chemistry, 35, 165-197, (2000)
Tensor RG calculations and quantum simulations near criticality
Meurice, Y; Tsai, Shan-Wen; Unmuth-Yockey, J; Yang, Li-Ping; Zhang, Jin
2016-01-01
We discuss the reformulation of the O(2) model with a chemical potential and the Abelian Higgs model on a 1+1 dimensional space-time lattice using the Tensor Renormalization Group (TRG) method. The TRG allows exact blocking and connects smoothly the classical Lagrangian approach to the quantum Hamiltonian approach. We calculate the entanglement entropy in the superfluid phase of the O(2) model and show that it approximately obeys the logarithmic Calabrese-Cardy scaling obtained from Conformal Field Theory (CFT). We calculate the Polyakov loop in the Abelian Higgs model and discuss the possibility of a deconfinement transition at finite volume. We propose Bose-Hubbard Hamiltonians implementable on optical lattices as quantum simulators for CFT models.
Quantum Statistical Calculation of Exchange Bias
Institute of Scientific and Technical Information of China (English)
WANG Huai-Yu; DAI Zhen-Hong
2004-01-01
The phenomenon of exchange bias of ferromagnetic (FM) films, which are coupled with an antiferromagnetic (AFM) film, is studied by Heisenberg model by use of the many-body Green's function method of quantum statistical theory for the uncompensated case. Exchange bias HE and coercivity Hc are calculated as functions of the FM film thickness L, temperature, the strength of the exchange interaction across the interface between FM and AFM and the anisotropy of the FM. Hc decreases with increasing L when the FM film is beyond some thickness. The dependence of the exchange bias HE on the FM film thickness and on temperature is also qualitatively in agreement with experiments.
Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P
2017-03-07
The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.
Quantum dynamics of fast chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Light, J.C. [Univ. of Chicago, IL (United States)
1993-12-01
The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.
Quantum chemical treatments of metal clusters.
Weigend, Florian; Ahlrichs, Reinhart
2010-03-28
This work focuses on finding and rationalizing the building principles of clusters with approximately 300 atoms of different types of metals: main group elements (Al, Sn), alkaline earth metals (Mg), transition metals (Pd) and clusters consisting of two different elements (Ir and Pt). Two tools are inevitable for this purpose: (i) quantum chemical methods that are able to treat a given cluster with both sufficient accuracy and efficiency and (ii) algorithms that are able to systematically scan the (3n-6)-dimensional potential surface of an n-atomic cluster for promising isomers. Currently, the only quantum chemical method that can be applied to metal clusters is density functional theory (DFT). Other methods either do not account for the multi-reference character of metal clusters or are too expensive and thus can be applied only to clusters of very few atoms, which usually is not sufficient for studying the building principles. The accuracy of DFT is not known a priori, but extrapolations to bulk values from calculated series of data show satisfying agreement with experimental data. For scans of the potential surface, simulated annealing techniques or genetic algorithms were used for the smaller clusters (approx. 20-30 atoms), and for the larger clusters considerations were restricted to selected packings and shapes. For the mixed-metallic clusters, perturbation theory turned out to be efficient and successful for finding the most promising distributions of the two atom types at the different sites.
Chemical Reactivity as Described by Quantum Chemical Methods
Directory of Open Access Journals (Sweden)
F. De Proft
2002-04-01
Full Text Available Abstract: Density Functional Theory is situated within the evolution of Quantum Chemistry as a facilitator of computations and a provider of new, chemical insights. The importance of the latter branch of DFT, conceptual DFT is highlighted following Parr's dictum "to calculate a molecule is not to understand it". An overview is given of the most important reactivity descriptors and the principles they are couched in. Examples are given on the evolution of the structure-property-wave function triangle which can be considered as the central paradigm of molecular quantum chemistry to (for many purposes a structure-property-density triangle. Both kinetic as well as thermodynamic aspects can be included when further linking reactivity to the property vertex. In the field of organic chemistry, the ab initio calculation of functional group properties and their use in studies on acidity and basicity is discussed together with the use of DFT descriptors to study the kinetics of SN2 reactions and the regioselectivity in Diels Alder reactions. Similarity in reactivity is illustrated via a study on peptide isosteres. In the field of inorganic chemistry non empirical studies of adsorption of small molecules in zeolite cages are discussed providing Henry constants and separation constants, the latter in remarkable good agreement with experiments. Possible refinements in a conceptual DFT context are presented. Finally an example from biochemistry is discussed : the influence of point mutations on the catalytic activity of subtilisin.
The many roles of quantum chemical predictions in synthetic organic chemistry.
Nguyen, Quynh Nhu N; Tantillo, Dean J
2014-03-01
This account discusses representative case studies for various applications of quantum chemical calculations in synthetic organic chemistry. These include confirmation of target structures, methodology development, and catalyst design. These examples demonstrate how predictions from quantum chemical calculations can be utilized to streamline synthetic efforts.
Wavelet Scattering Regression of Quantum Chemical Energies
Hirn, Matthew; Poilvert, Nicolas
2016-01-01
We introduce multiscale invariant dictionaries to estimate quantum chemical energies of organic molecules, from training databases. Molecular energies are invariant to isometric atomic displacements, and are Lipschitz continuous to molecular deformations. Similarly to density functional theory (DFT), the molecule is represented by an electronic density function. A multiscale invariant dictionary is calculated with wavelet scattering invariants. It cascades a first wavelet transform which separates scales, with a second wavelet transform which computes interactions across scales. Sparse scattering regressions give state of the art results over two databases of organic planar molecules. On these databases, the regression error is of the order of the error produced by DFT codes, but at a fraction of the computational cost.
Śmiszek-Lindert, Wioleta Edyta; Chełmecka, Elżbieta; Góralczyk, Stefan; Kaczmarek, Marian
2017-01-01
Theoretical calculations of the m-acetotoluidide and m-thioacetotoluidide isolated molecules were performed by using density functional theory (DFT) method at B3LYP/6-311++G (d,p) and B3LYP/6-311++G (3df,2pd) basis set levels. The Hirshfeld surfaces analysis and FT-IR and FT-Raman spectroscopy studies have been reported. The geometrical parameters of the title amide and thioamide are in a good agreement with the XRD experiment. The vibrational frequencies were calculated and scaled, and subsequently values have been compared with the experimental Infrared and Raman spectra. The observed and calculated frequencies are found to be in good agreement. The analysis of the Hirshfeld surface has been well correlated to the spectroscopic studies. Additionally, the highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO) and the energy gap between EHOMO and ELUMO (ΔEHOMO-LUMO) have been calculated.
2008-01-01
The molecular structures of methylphosphine (CH3PH2) and methylphosphine-borane (CH3PH2·BH3) have been determined from gas-phase electron diffraction data and rotational constants, employing the SARACEN method. The experimental geometric parameters generally showed a good agreement with those obtained using ab initio calculations and previous microwave spectroscopy studies. In order to assess the accuracy of the calculated structures a range of ab initio methods were used, including the CCSD(...
Quantum Monte Carlo Calculations of Neutron Matter
Carlson, J; Ravenhall, D G
2003-01-01
Uniform neutron matter is approximated by a cubic box containing a finite number of neutrons, with periodic boundary conditions. We report variational and Green's function Monte Carlo calculations of the ground state of fourteen neutrons in a periodic box using the Argonne $\\vep $ two-nucleon interaction at densities up to one and half times the nuclear matter density. The effects of the finite box size are estimated using variational wave functions together with cluster expansion and chain summation techniques. They are small at subnuclear densities. We discuss the expansion of the energy of low-density neutron gas in powers of its Fermi momentum. This expansion is strongly modified by the large nn scattering length, and does not begin with the Fermi-gas kinetic energy as assumed in both Skyrme and relativistic mean field theories. The leading term of neutron gas energy is ~ half the Fermi-gas kinetic energy. The quantum Monte Carlo results are also used to calibrate the accuracy of variational calculations ...
Quantum Chemical Strain Analysis For Mechanochemical Processes.
Stauch, Tim; Dreuw, Andreas
2017-03-24
The use of mechanical force to initiate a chemical reaction is an efficient alternative to the conventional sources of activation energy, i.e., heat, light, and electricity. Applications of mechanochemistry in academic and industrial laboratories are diverse, ranging from chemical syntheses in ball mills and ultrasound baths to direct activation of covalent bonds using an atomic force microscope. The vectorial nature of force is advantageous because specific covalent bonds can be preconditioned for rupture by selective stretching. However, the influence of mechanical force on single molecules is still not understood at a fundamental level, which limits the applicability of mechanochemistry. As a result, many chemists still resort to rules of thumb when it comes to conducting mechanochemical syntheses. In this Account, we show that comprehension of mechanochemistry at the molecular level can be tremendously advanced by quantum chemistry, in particular by using quantum chemical force analysis tools. One such tool is the JEDI (Judgement of Energy DIstribution) analysis, which provides a convenient approach to analyze the distribution of strain energy in a mechanically deformed molecule. Based on the harmonic approximation, the strain energy contribution is calculated for each bond length, bond angle and dihedral angle, thus providing a comprehensive picture of how force affects molecules. This Account examines the theoretical foundations of quantum chemical force analysis and provides a critical overview of the performance of the JEDI analysis in various mechanochemical applications. We explain in detail how this analysis tool is to be used to identify the "force-bearing scaffold" of a distorted molecule, which allows both the rationalization and the optimization of diverse mechanochemical processes. More precisely, we show that the inclusion of every bond, bending and torsion of a molecule allows a particularly insightful discussion of the distribution of mechanical
Quantum chemical investigation of mechanisms of silane oxidation
DEFF Research Database (Denmark)
Mader, Mary M.; Norrby, Per-Ola
2001-01-01
Several mechanisms for the peroxide oxidation of organosilanes to alcohols are compared by quantum chemical calculations, including solvation with the PCM method. Without doubt, the reaction proceeds via anionic, pentacoordinate silicate species, but a profound difference is found between in vacuo...
Quantum theory of chemical reaction rates
Energy Technology Data Exchange (ETDEWEB)
Miller, W.H. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States). Chemical Sciences Div.
1994-10-01
If one wishes to describe a chemical reaction at the most detailed level possible, i.e., its state-to-state differential scattering cross section, then it is necessary to solve the Schroedinger equation to obtain the S-matrix as a function of total energy E and total angular momentum J, in terms of which the cross sections can be calculated as given by equation (1) in the paper. All other physically observable attributes of the reaction can be derived from the cross sections. Often, in fact, one is primarily interested in the least detailed quantity which characterizes the reaction, namely its thermal rate constant, which is obtained by integrating Eq. (1) over all scattering angles, summing over all product quantum states, and Boltzmann-averaging over all initial quantum states of reactants. With the proper weighting factors, all of these averages are conveniently contained in the cumulative reaction probability (CRP), which is defined by equation (2) and in terms of which the thermal rate constant is given by equation (3). Thus, having carried out a full state-to-state scattering calculation to obtain the S-matrix, one can obtain the CRP from Eq. (2), and then rate constant from Eq. (3), but this seems like ``overkill``; i.e., if one only wants the rate constant, it would clearly be desirable to have a theory that allows one to calculate it, or the CRP, more directly than via Eq. (2), yet also correctly, i.e., without inherent approximations. Such a theory is the subject of this paper.
Quantum biological channel modeling and capacity calculation.
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.
Quantum Biological Channel Modeling and Capacity Calculation
Directory of Open Access Journals (Sweden)
Ivan B. Djordjevic
2012-12-01
Full Text Available 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.
Sinha, L; Prasad, O; Chand, S; Sachan, A K; Pathak, S K; Shukla, V K; Karabacak, M; Asiri, A M
2014-12-10
FT-IR and FT-Raman spectra of anethole (1-Methoxy-4-(1-propenyl)benzene), a flavoring agent of commercial value, have been recorded in the regions 4000-400 and 4000-100cm(-1) respectively. The structure of the title molecule has been optimized and the structural parameters have been calculated by DFT/B3LYP method with 6-311++G(d,p) basis set. The fundamental vibrational wavenumbers as well as their intensities were calculated and a good agreement between observed and scaled calculated wavenumbers has been achieved. UV-Vis spectrum of the title compound was recorded in the region 200-500nm and the electronic properties such as HOMO and LUMO energies and associated energy gap were calculated by Time dependent-density functional theory (TD-DFT) approach. Nonlinear optical (NLO) study divulges the nonlinear properties of the molecule. Stability of the title molecule arising from hyper-conjugative interactions and charge delocalization has been investigated using natural bond orbital (NBO) analysis. The theoretical results were found to be in coherence with the measured experimental data. Copyright © 2014 Elsevier B.V. All rights reserved.
Ganapathy, S; Fournier, M; Paul, J F; Delevoye, L; Guelton, M; Amoureux, J P
2002-07-03
HeteroPolyAcids (HPA's) are a class of solid acids that have broad applications in many fields of science and technology, including catalysis and chemical engineering. The proton locations within the thermally stable and commonly known Keggin unit, which is the primary structure building unit/block, has remained undetermined in anhydrous HPAs, despite numerous theoretical and experimental efforts. However, Rotational Echo DOuble Resonance (REDOR) NMR and Density Functional Theory (DFT) quantum chemical calculations offer a new opportunity to determine the exact locations of protons within the Keggin unit. The crucial experimental evidence is provided for the basic and very extensively studied acidic form of H(8-n)X(n+)M(12)O(40), X = Si, P and M = Mo, W, belonging to the Keggin structure. While showing that the acidic protons are located in the bridging oxygen positions (R(P-H) = 520 +/- 20 pm) in H(3)PMo(12)O(40) and in the terminal oxygen positions (R(P-H) = 570 +/- 20 pm) in H(3)PW(12)O(40), REDOR measurements also provide for the first time the structural basis to consistently rank the acid strength for the important class of Keggin solid catalysts.
Eryılmaz, Serpil; Gül, Melek; İnkaya, Ersin; İdil, Önder; Özdemir, Namık
2016-10-01
In this paper, 3-(4-chlorophenyl)-3a,4,7,7a-tetrahydro-4,7-methanobenzo[d]isoxazole was synthesized via 1,3 dipolar cycloaddition, characterized by spectroscopic analysis such as FT-IR, 1H NMR, 13C NMR, UV-Vis, LC-MS/MS, Elemental Analysis, and X-ray Single Crystal diffraction technique. The Density Functional Theory (DFT/B3LYP) method with 6-311G(d,p) basis set in the ground state was applied for quantum chemical calculations and molecular geometric parameters of the compound were compared with the X-ray analysis results. FT-IR, NMR and UV-Vis spectral analysis were analysed to determine the compliance with the vibrational frequencies, 1H NMR and 13C NMR chemical shifts and absorption wavelength values. The frontier molecular orbitals (FMOs), some global reactivity descriptors, molecular electrostatic potential (MEP), thermodynamic properties, non-linear optical (NLO) behaviour of the compound were examined with the same method in gas phase, theoretically. Moreover, antioxidant activity was determined with three different methods - DPPH radical scavenging, reducing and metal chelating, antimicrobial activity were carried out with Gram positive, Gram negative and Eukaryote for the title compound.
Quantum Theory of Fast Chemical Reactions
Energy Technology Data Exchange (ETDEWEB)
Light, John C
2007-07-30
The aims of the research under this grant were to develop a theoretical understanding and predictive abiility for a variety of processes occurring in the gas phase. These included bimolecular chemical exchange reactions, photodissociation, predissociation resonances, unimolecular reactions and recombination reactions. In general we assumed a knowledge, from quantum chemistry, of the interactions of the atoms and molecular fragments involved. Our focus was primarily on the accurate (quantum) dynamics of small molecular systems. This has been important for many reactions related to combustion and atmospheric chemistry involving light atom transfer reactions and, for example, resonances in dissociation and recombination reactions. The rates of such reactions, as functions of temperature, internal states, and radiation (light), are fundamental for generating models of overall combustion processes. A number of new approaches to these problems were developed inclluding the use of discrete variable representations (DVR's) for evaluating rate constants with the flux-flux correlation approach, finite range approaches to exact quantum scattering calculations, energy selected basis representations, transition state wave packet approaches and improved semiclassical approaches. These (and others) were applied to a number of reactive systems and molecular systems of interest including (many years ago) the isotopic H + H2 exchange reactions, the H2 + OH (and H + H2O) systems, Ozone resonances, van der Waals molecule reactions, etc. A total of 7 graduate students, and 5 post-doctoral Research Associates were supported, at least in part, under this grant and seven papers were published with a total of 10 external collaborators. The majority of the 36 publications under this grant were supported entirely by DOE.
Quantum-chemical studies of metal oxides for photoelectrochemical applications
Persson, P.; Bergström, R.; Ojamäe, L.; Lunell, S.
A review of recent research, as well as new results, are presented on transition metal oxide clusters, surfaces, and crystals. Quantum-chemical calculations of clusters of first row transition metal oxides have been made to evaluate the accuracy of ab initio and density functional calculations. Adsorbates on metal oxide surfaces have been studied with both ab initio and semi-empirical methods, and results are presented for the bonding and electronic interactions of large organic adsorbates, e.g. aromatic molecules, on Ti02 and ZnO. Defects and intercalation, notably of H, Li, and Na in Ti02 have been investigated theoretically. Comparisons with experiments are made throughout to validate the calculations. Finally, the role of quantum-chemical calculations in the study of metal oxide based photoelectrochemical devices, such as dyesensitized solar cells and electrochromic displays. is discussed.
Bruhn, Torsten; Witterauf, Franziska; Götz, Daniel C G; Grimmer, Carina T; Würtemberger, Max; Radius, Udo; Bringmann, Gerhard
2014-04-01
β,β'-Bisporphyrins are intrinsically chiral porphyrin dimers with fascinating properties. The configurational stability at their axes can be directed by variation of the central metal atoms. Herein, we present a regioselective functionalization of the monomeric 2-amino-tetraphenyl-porphyrin as a versatile substrate for dimerization by oxidative coupling. By simple variation of the reaction conditions (solvent and oxidant), the oxidation selectively gave either the axially chiral C,C-coupled diaminobisporphyrin in high yields or, under Ullmann conditions, the twofold N,C-linked achiral dimer, also in good yields. A generalized mechanism for the coupling reaction is proposed based on DFT calculations. The axially chiral β,β'-coupled porphyrin dimers were isolated as racemic mixtures, but can be resolved by HPLC on a chiral phase. TDDFT and coupled-cluster calculations were used to explain the spectroscopic properties of the aminoporphyrins and their dimers and to elucidate the absolute configurations of the C,C-coupled bisporphyrins.
Energy Technology Data Exchange (ETDEWEB)
Pustovarov, V. A. [Ural State Technical University (Russian Federation); Aliev, V. Sh.; Perevalov, T. V., E-mail: timson@isp.nsc.ru; Gritsenko, V. A., E-mail: grits@isp.nsc.ru [Russian Academy of Sciences, Institute of Semiconductor Physics, Siberian Branch (Russian Federation); Eliseev, A. P. [Russian Academy of Sciences, Institute of Geology and Mineralogy, Siberian Branch (Russian Federation)
2010-01-15
The electronic structure of an oxygen vacancy in {alpha}-Al{sub 2}O{sub 3} and {gamma}-Al{sub 2}O{sub 3} is calculated. The calculation predicts an absorption peak at an energy of 6.4 and 6.3 eV in {alpha}-Al{sub 2}O{sub 3} and {gamma}-Al{sub 2}O{sub 3}, respectively. The luminescence and luminescence excitation spectra of amorphous Al{sub 2}O{sub 3} are measured using synchrotron radiation. The presence of a luminescence band at 2.9 eV and a peak at 6.2 eV in the luminescence excitation spectrum indicates the presence of oxygen vacancies in amorphous Al{sub 2}O{sub 3}.
Suresh, S; Gunasekaran, S; Srinivasan, S
2014-05-05
The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Cech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbová, Marie; Jurečka, Petr; Sponer, Jiří
2013-05-21
The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by ΔCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important families of DNA backbone conformations and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar-phosphate-sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-ζ basis set, which is, however, computationally very demanding. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as
Quantum chemical studies of estrogenic compounds
Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...
Drużbicki, Kacper; Mikuli, Edward; Kocot, Antoni; Ossowska-Chruściel, Mirosława Danuta; Chruściel, Janusz; Zalewski, Sławomir
2012-08-02
The experimental and theoretical vibrational spectroscopic study of one of a novel antiferroelectric liquid crystals (AFLC), known under the MHPSBO10 acronym, have been undertaken. The interpretation of both FT-IR and FT-Raman spectra was focused mainly on the solid-state data. To analyze the experimental results along with the molecular properties, density functional theory (DFT) computations were performed using several modern theoretical approaches. The presented calculations were performed within the isolated molecule model, probing the performance of modern exchange-correlations functionals, as well as going beyond, i.e., within hybrid (ONIOM) and periodic boundary conditions (PBC) methodologies. A detailed band assignment was supported by the normal-mode analysis with SQM ab initio force field scaling. The results are supplemented by the noncovalent interactions analysis (NCI). The relatively noticeable spectral differences observed upon Crystal to AFLC phase transition have also been reported. For the most prominent vibrational modes, the geometries of the transition dipole moments along with the main components of vibrational polarizability were analyzed in terms of the molecular frame. One of the goals of the paper was to optimize the procedure of solid-state calculations to obtain the results comparable with the all electron calculations, performed routinely for isolated molecules, and to test their performance. The presented study delivers a complex insight into the vibrational spectrum with a noticeable improvement of the theoretical results obtained for significantly attracting mesogens using modern molecular modeling approaches. The presented modeling conditions are very promising for further description of similar large molecular crystals.
DEFF Research Database (Denmark)
Hansen, Bjarke Knud Vilster; Møller, Søren; Spanget-Larsen, Jens
2006-01-01
The title compound (DPB) was investigated by FTIR spectroscopy in liquid solutions and by FTIR linear dichroism (LD) measurements on samples aligned in stretched polyethylene. The LD data provided experimental assignments of molecular transition moment directions and vibrational symmetries for more...... than 40 vibrational transitions. The observed IR wavenumbers, relative intensities, and polarization directions were generally well reproduced by the results of a harmonic analysis based on B3LYP/cc-pVTZ density functional theory (DFT). The combined experimental and theoretical results led to proposal...... of a nearly complete assignment of the IR active fundamentals of DPB, involving reassignment of a number of transitions. In addition, previously published Raman spectra of DPB were well predicted by the B3LYP/cc-pVTZ calculations....
Energy Technology Data Exchange (ETDEWEB)
Finsgar, Matjaz; Lesar, Antonija; Kokalj, Anton [Jozef Stefan Institute, Department of Physical and Organic Chemistry, Jamova cesta 39, SI-1000 Ljubljana (Slovenia); Milosev, Ingrid [Jozef Stefan Institute, Department of Physical and Organic Chemistry, Jamova cesta 39, SI-1000 Ljubljana (Slovenia); Valdoltra Orthopaedic Hospital, Jadranska c. 31, SI-6280 Ankaran (Slovenia)], E-mail: ingrid.milosev@ijs.si
2008-11-30
The inhibition of copper corrosion in 3% NaCl solution was studied by using a well-known inhibitor, benzotriazole (BTAH), and its not so extensively explored derivative, 1-hydroxybenzotriazole (BTAOH). Electrochemical methods, i.e., linear polarization, Tafel and potentiodynamic curve measurements and electrochemical quartz crystal microbalance (EQCM) measurements were used. Corrosion parameters and inhibition effectiveness were determined. Experimental results showed that benzotriazole is a more effective inhibitor of the corrosion of copper in chloride media than 1-hydroxybenzotriazole. Whereas in the presence of BTAH a protective Cu-BTA layer is formed on the Cu surface, in the presence of BTAOH a thick, poorly protective layer is formed, which readily dissolves in chloride solution. Kinetic parameters were calculated based on EQCM results. Adsorption of BTAOH follows a linear growth law, in contrast to BTAH, whose film growth can be best represented at first by a parabolic, and later by logarithmic, growth law. Different mechanisms of growth imply different mechanisms of inhibition and account for the different inhibition effectiveness. Density functional theory calculations were performed to characterize certain features of the molecular structures, including the electronic parameters related to the inhibition effectiveness of these inhibitors. Introduction of the -OH group into the benzotriazole molecules does not change their electronic parameters significantly neither in gas phase nor in the presence of water solvent. Other parameters, therefore, affect the inhibition effectiveness of these corrosion inhibitors. In particular, superior inhibition effectiveness of BTAH is attributed to interplay of planar molecular structure, physisorption and intermolecular H-bonding, which cooperatively may result in formation of thin and protective film on the surface.
Retrocausality in Quantum Phenomena and Chemical Evolution
Directory of Open Access Journals (Sweden)
Koichiro Matsuno
2016-10-01
Full Text Available The interplay between retrocausality and the time-reversal symmetry of the dynamical law of quantum mechanics underscores the significance of the measurement dynamics with the use of indivisible and discrete quantum particles to be mediated. One example of empirical evidence demonstrating the significance of retrocausality going along with time-reversal symmetry is seen in the operation of a reaction cycle to be expected in chemical evolution. A reaction cycle can hold itself when the causative operation of the cycle remains robust, even when facing frequent retrocausal interventions of a quantum-mechanical origin. Quantum mechanics in and of itself has potential in raising a reaction cycle in the prebiotic phase of chemical evolution, even without any help of artefactual scaffoldings of an external origin.
Sensitive chemical compass assisted by quantum criticality
Cai, C. Y.; Ai, Qing; Quan, H. T.; Sun, C. P.
2012-02-01
A radical-pair-based chemical reaction might be used by birds for navigation via the geomagnetic direction. The inherent physical mechanism is that the quantum coherent transition from a singlet state to triplet states of the radical pair could respond to a weak magnetic field and be sensitive to the direction of such a field; this then results in different photopigments to be sensed by the avian eyes. Here, we propose a quantum bionic setup, inspired by the avian compass, as an ultrasensitive probe of a weak magnetic field based on the quantum phase transition of the environments of the two electrons in the radical pair. We prove that the yield of the chemical products via recombination from the singlet state is determined by the Loschmidt echo of the environments with interacting nuclear spins. Thus quantum criticality of environments could enhance the sensitivity of detection of weak magnetic fields.
Sensitive Chemical Compass Assisted by Quantum Criticality
Cai, C Y; Quan, H T; Sun, C P
2011-01-01
The radical-pair-based chemical reaction could be used by birds for the navigation via the geomagnetic direction. An inherent physical mechanism is that the quantum coherent transition from a singlet state to triplet states of the radical pair could response to the weak magnetic field and be sensitive to the direction of such a field and then results in different photopigments in the avian eyes to be sensed. Here, we propose a quantum bionic setup for the ultra-sensitive probe of a weak magnetic field based on the quantum phase transition of the environments of the two electrons in the radical pair. We prove that the yield of the chemical products via the recombination from the singlet state is determined by the Loschmidt echo of the environments with interacting nuclear spins. Thus quantum criticality of environments could enhance the sensitivity of the detection of the weak magnetic field.
Ma, Cong; Huang, Jie; Ma, Hai-Xia; Xu, Kang-Zhen; Lv, Xing-Qiang; Song, Ji-Rong; Zhao, Ning-Ning; He, Jian-Yun; Zhao, Yi-Sha
2013-03-01
A novel potassium complex has been synthesized and characterized under the non-isothermal conditions by DSC and TG-DTG method. The 4,4-azo-1,2,4-triazol-5-one (ZTO) has the molecular formula C4H4N8O2. The thermodynamic parameters, HOMO-LUMO energy gap, total energy and electrostatic potential (MEP) of ZTO are conducted by density functional theory DFT/B3LYP calculation method with 6-311G basis set. In the coordination polymer, with the ligand anion (ZTO-) as space linkers, two types of potassium atoms centers are joined together to form three-dimensional frameworks. The enthalpy, apparent activation energy and pre-exponential factor of the second exothermic decomposition reaction are 85.43 kJ mol-1, 414.4 kJ mol-1and 1037.92 s-1, respectively. The critical temperature of thermal explosion (Tb) for [K(ZTO)ṡH2O]∞ is 275.08 °C. [K(ZTO)ṡH2O]∞ CCDC: 902339.
Lamhasni, T; Ait Lyazidi, S; Hnach, M; Haddad, M; Desmaële, D; Spanget-Larsen, J; Nguyen, D D; Ducasse, L
2013-09-01
The photophysical properties of the antiviral 7-nicotinoyl-styrylquinoline (MB96) were investigated by means of UV-Vis linear dichroism (LD) spectroscopy on molecular samples aligned in stretched polyvinylalcohol (PVA), supported by time dependent density functional theory (TD-DFT) calculations. Experimentally, the directions of the transitions moments with respect to the long axis of the molecule were deduced from the orientation K factors, determined by means of "trial-and-error" procedure. The absorption spectrum presents two parts. The main transition in the lowest energy part, observed around 365 nm and showing the highest K value 0.8, is longitudinally in-plane polarized. The highest energy part which is extended between 230 and 320 nm, large, diffuse, and of weak intensity, shows estimated K values between 0.2 and 0.5. This complex structure is transversally polarized with some contamination by the longitudinal character of the first strong band. The TD-DFT results agree fairly well with the LD measurements.
Accelerating Wave Function Convergence in Interactive Quantum Chemical Reactivity Studies
Mühlbach, Adrian H; Reiher, Markus
2015-01-01
The inherently high computational cost of iterative self-consistent-field (SCF) methods proves to be a critical issue delaying visual and haptic feedback in real-time quantum chemistry. In this work, we introduce two schemes for SCF acceleration. They provide a guess for the initial density matrix of the SCF procedure generated by extrapolation techniques. SCF optimizations then converge in fewer iterations, which decreases the execution time of the SCF optimization procedure. To benchmark the proposed propagation schemes, we developed a test bed for performing quantum chemical calculations on sequences of molecular structures mimicking real-time quantum chemical explorations. Explorations of a set of six model reactions employing the semi-empirical methods PM6 and DFTB3 in this testing environment showed that the proposed propagation schemes achieved speedups of up to thirty percent as a consequence of a reduced number of SCF iterations.
Approaching Chemical Accuracy with Quantum Monte Carlo
Petruzielo, F R; Umrigar, C J
2012-01-01
A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space.
Use of ab initio quantum chemical methods in battery technology
Energy Technology Data Exchange (ETDEWEB)
Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.
Wallevik, Sunna O; Bjornsson, Ragnar; Kvaran, Agúst; Jonsdottir, Sigridur; Arnason, Ingvar; Belyakov, Alexander V; Baskakov, Alexander A; Hassler, Karl; Oberhammer, Heinz
2010-02-11
The molecular structure of axial and equatorial conformers of 1-silyl-silacyclohexane, C(5)H(10)SiHSiH(3), and the thermodynamic equilibrium between these species were investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR), temperature-dependent Raman spectroscopy, and quantum chemical calculations (CCSD(T), MP2 and DFT methods). According to GED, the compound exists as a mixture of two conformers possessing the chair conformation of the six-membered ring and C(s) symmetry and differing in the axial or equatorial position of the SiH(3) group (axial = 57(7) mol %/equatorial = 43(7) mol %) at T = 321 K. This corresponds to an A value (free energy difference = G(axial) - G(equatorial)) of -0.17(15) kcal mol(-1). A low-temperature (13)C NMR experiment using SiD(4) as a solvent resulted in an axial/equatorial ratio of 45(3)/55(3) mol % at 110 K corresponding to an A value of 0.05(3) kcal mol(-1), and a DeltaG(#) value of 5.7(2) kcal mol(-1) was found at 124 K. Temperature-dependent Raman spectroscopy in the temperature range of 210-300 K of the neat liquid, a THF solution, and a heptane solution indicates that the axial conformer is favored over the equatorial one by 0.26(10), 0.23(10), and 0.22(10) kcal mol(-1) (DeltaH values), respectively. CCSD(T)/CBS and MP2/CBS calculations in general predict both conformations to have very similar stability and are, thus, in excellent agreement with the DNMR result but in a slight disagreement with the GED and Raman results. Two DFT functionals, that account for dispersion interactions, M06-2X/pc-3 and B2PLYP-D/QZVPP, deviate from the high-level coupled cluster and MP2 calculations by only 0.1 kcal mol(-1) on average, whereas B3LYP/pc-3 calculations greatly overestimate the stability of the equatorial conformer.
Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Gray, S.K. [Argonne National Laboratory, IL (United States)
1993-12-01
A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.
Li, Shenggang; Zhai, Hua-Jin; Wang, Lai-Sheng; Dixon, David A
2012-05-31
Anion photoelectron spectroscopy and quantum chemical calculations at the density functional theory (DFT), coupled cluster theory (CCSD(T)), and complete active space self-consistent field (CASSCF) theory levels are employed to study the reduced transition metal oxide clusters M(4)O(10)(-) (M = Cr, W) and their neutrals. Photoelectron spectra are obtained at 193 and 157 nm photon energies, revealing very different electronic structures for the Cr versus W oxide clusters. The electron affinity and HOMO-LUMO gap are measured to be 3.68 ± 0.05 and 0.7 eV, respectively, for the Cr(4)O(10) neutral cluster, as compared to 4.41 ± 0.04 and 1.3 eV for W(4)O(10). A comprehensive search is performed to determine the ground-state structures for M(4)O(10) and M(4)O(10)(-), in terms of geometry and electronic states by carefully examining the calculated relative energies at the DFT, CCSD(T), and CASSCF levels. The ground states of Cr(4)O(10) and Cr(4)O(10)(-) have tetrahedral structures similar to that of P(4)O(10) with the anion having a lower symmetry due to a Jahn-Teller distortion. The ground states of W(4)O(10) and W(4)O(10)(-) have butterfly shape structures, featuring two fused five-member rings with a metal-metal multiple bond between the central metal atoms. The much stronger WW bonding than the CrCr bonding is found to be the primary cause for the different ground state structures of the reduced Cr(4)O(10)(0/-) versus W(4)O(10)(0/-) oxide clusters. The photoelectron spectra are assigned by comparing the experimental and theoretical adiabatic and vertical electron detachment energies, further confirming the determination of the ground electronic states of M(4)O(10) and M(4)O(10)(-). The time-dependent DFT method is used to calculate the excitation energies of M(4)O(10). The TD-DFT results in combination with the self-consistently calculated vertical detachment energies for some of the excited states at the DFT and CCSD(T) levels are used to assign the higher energy
Wedler, Henry B; Pemberton, Ryan P; Lounnas, Valère; Vriend, Gert; Tantillo, Dean J; Wang, Selina C
2015-05-01
Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined.
Wedler, H.B.; Pemberton, R.P.; Lounnas, V.; Vriend, G.; Tantillo, D.J.; Wang, S.C.
2015-01-01
Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined.
Molecular orbital calculations using chemical graph theory
Dias, Jerry Ray
1993-01-01
Professor John D. Roberts published a highly readable book on Molecular Orbital Calculations directed toward chemists in 1962. That timely book is the model for this book. The audience this book is directed toward are senior undergraduate and beginning graduate students as well as practicing bench chemists who have a desire to develop conceptual tools for understanding chemical phenomena. Although, ab initio and more advanced semi-empirical MO methods are regarded as being more reliable than HMO in an absolute sense, there is good evidence that HMO provides reliable relative answers particularly when comparing related molecular species. Thus, HMO can be used to rationalize electronic structure in 1t-systems, aromaticity, and the shape use HMO to gain insight of simple molecular orbitals. Experimentalists still into subtle electronic interactions for interpretation of UV and photoelectron spectra. Herein, it will be shown that one can use graph theory to streamline their HMO computational efforts and to arrive...
Calculation of the energetics of chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Dunning, T.H. Jr.; Harding, L.B.; Shepard, R.L.; Harrison, R.J.
1988-01-01
To calculate the energetics of chemical reactions we must solve the electronic Schroedinger equation for the molecular conformations of importance for the reactive encounter. Substantial changes occur in the electronic structure of a molecular system as the reaction progresses from reactants through the transition state to products. To describe these changes, our approach includes the following three elements: the use of multiconfiguration self-consistent field wave functions to provide a consistent zero-order description of the electronic structure of the reactants, transition state, and products; the use of configuration interaction techniques to describe electron correlation effects needed to provide quantitative predictions of the reaction energetics; and the use of large, optimized basis sets to provide the flexibility needed to describe the variations in the electronic distributions. With this approach we are able to study reactions involving as many as 5--6 atoms with errors of just a few kcal/mol in the predicted reaction energetics. Predictions to chemical accuracy, i.e., to 1 kcal/mol or less, are not yet feasible, although continuing improvements in both the theoretical methodology and computer technology suggest that this will soon be possible, at least for reactions involving small polyatomic species. 4 figs.
Monte-carlo calculations for some problems of quantum mechanics
Energy Technology Data Exchange (ETDEWEB)
Novoselov, A. A., E-mail: novoselov@goa.bog.msu.ru; Pavlovsky, O. V.; Ulybyshev, M. V. [Moscow State University (Russian Federation)
2012-09-15
The Monte-Carlo technique for the calculations of functional integral in two one-dimensional quantum-mechanical problems had been applied. The energies of the bound states in some potential wells were obtained using this method. Also some peculiarities in the calculation of the kinetic energy in the ground state had been studied.
Vibrational Spectra and Quantum Calculations of Ethylbenzene
Institute of Scientific and Technical Information of China (English)
Jian Wang; Xue-jun Qiu; Yan-mei Wang; Song Zhang; Bing Zhang
2012-01-01
Normal vibrations of ethylbenzene in the first excited state have been studied using resonant two-photon ionization spectroscopy.The band origin of ethylbenzene of S1←S0 transition appeared at 37586 cm-1.A vibrational spectrum of 2000 cm-1 above the band origin in the first excited state has been obtained.Several chain torsions and normal vibrations are obtained in the spectrum.The energies of the first excited state are calculated by the time-dependent density function theory and configuration interaction singles (CIS) methods with various basis sets.The optimized structures and vibrational frequencies of the S0 and S1 states are calculated using Hartree-Fock and CIS methods with 6-311++G(2d,2p) basis set.The calculated geometric structures in the S0 and S1 states are gauche conformations that the symmetric plane of ethyl group is perpendicular to the ring plane.All the observed spectral bands have been successfully assigned with the help of our calculations.
Quantum chemical modeling of uranyl adsorption on mineral surfaces
Energy Technology Data Exchange (ETDEWEB)
Kremleva, A.; Krueger, S.; Roesch, N. [Dept. Chemie and Catalysis Research Center, Technische Univ. Muenchen, Garching (Germany)
2010-07-01
We overview quantum mechanical simulations that model the adsorption of actinide ions at solvated mineral surfaces. Pertinent examples illustrate the status of this emerging field of computational chemistry. In particular, we describe our own studies on uranyl adsorption on kaolinite. Already the few available results, from applications of density functional methods to cluster models or periodic slab models, show that such calculations are a useful complement to experimental investigations. Detailed information at the atomic level from accurate electronic structure calculations on well defined model systems helps to refine current interpretations of the chemical nature of uranyl adsorption species and to discover new features of these interface systems. Results from quantum mechanical simulations also provide a valuable reference for future experimental investigations. (orig.)
Quantum mechanical calculations and mineral spectroscopy
Kubicki, J. D.
2006-05-01
Interpretation of spectra in systems of environmental interest is not generally straightforward due to the lack of close analogs and a clear structure of some components of the system. Computational chemistry can be used as an objective method to test interpretations of spectra. This talk will focus on applying ab initio methods to complement vibrational, NMR, and EXAFS spectroscopic information. Examples of systems studied include phosphate/Fe-hydroxides, arsenate/Al- and Fe-hydroxide, fractured silica surfaces. Phosphate interactions with Fe-hydroxides are important in controlling nutrient availability in soils and transport within streams. In addition, organo-phosphate bonding may be a key attachment mechanism for bacteria at Fe-oxide surfaces. Interpretation of IR spectra is enhanced by model predictions of vibrational frequencies for various surface complexes. Ab initio calculations were used to help explain As(V) and As(III) adsorption behavior onto amorphous Al- and Fe-hydroxides in conjunction with EXAFS measurements. Fractured silica surfaces have been implicated in silicosis. These calculations test structures that could give rise to radical formation on silica surfaces. Calculations to simulate the creation of Si and SiO radical species on sufaces and their subsequent production of OH radicals will be discussed.
Efficient calculation of dissipative quantum transport properties in semiconductor nanostructures
Energy Technology Data Exchange (ETDEWEB)
Greck, Peter
2012-11-26
We present a novel quantum transport method that follows the non-equilibrium Green's function (NEGF) framework but side steps any self-consistent calculation of lesser self-energies by replacing them by a quasi-equilibrium expression. We termed this method the multi-scattering Buettiker-Probe (MSB) method. It generalizes the so-called Buettiker-Probe model but takes into account all relevant individual scattering mechanisms. It is orders of magnitude more efficient than a fully selfconsistent non-equilibrium Green's function calculation for realistic devices, yet accurately reproduces the results of the latter method as well as experimental data. This method is fairly easy to implement and opens the path towards realistic three-dimensional quantum transport calculations. In this work, we review the fundamentals of the non-equilibrium Green's function formalism for quantum transport calculations. Then, we introduce our novel MSB method after briefly reviewing the original Buettiker-Probe model. Finally, we compare the results of the MSB method to NEGF calculations as well as to experimental data. In particular, we calculate quantum transport properties of quantum cascade lasers in the terahertz (THz) and the mid-infrared (MIR) spectral domain. With a device optimization algorithm based upon the MSB method, we propose a novel THz quantum cascade laser design. It uses a two-well period with alternating barrier heights and complete carrier thermalization for the majority of the carriers within each period. We predict THz laser operation for temperatures up to 250 K implying a new temperature record.
Chemical accuracy from quantum Monte Carlo for the benzene dimer
Energy Technology Data Exchange (ETDEWEB)
Azadi, Sam, E-mail: s.azadi@ucl.ac.uk [Department of Earth Science and Thomas Young Centre, University College London, London WC1E 6BT (United Kingdom); Cohen, R. E. [London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom and Extreme Materials Initiative, Geophysical Laboratory, Carnegie Institution of Washington, Washington, D.C. 20015 (United States)
2015-09-14
We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of −2.3(4) and −2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is −2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.
Ikeda, Atsushi; Hennig, Christoph; Rossberg, André; Tsushima, Satoru; Scheinost, Andreas C; Bernhard, Gert
2008-02-15
A multitechnique approach using extended X-ray absorption fine structure (EXAFS) spectroscopy based on iterative transformation factor analysis (ITFA), UV-visible absorption spectroscopy, and density functional theory (DFT) calculations has been performed in order to investigate the speciation of uranium(VI) nitrate species in acetonitrile and to identify the complex structure of individual species in the system. UV-visible spectral titration suggests that there are four different species in the system, that is, pure solvated species, mono-, di-, and trinitrate species. The pure EXAFS spectra of these individual species are extracted by ITFA from the measured spectral mixtures on the basis of the speciation distribution profile calculated from the UV-visible data. Data analysis of the extracted EXAFS spectra, with the help of DFT calculations, reveals the most probable complex structures of the individual species. The pure solvated species corresponds to a uranyl hydrate complex with an equatorial coordination number (CNeq) of 5, [UO2(H2O)5]2+. Nitrate ions tend to coordinate to the uranyl(VI) ion in a bidentate fashion rather than a unidentate one in acetonitrile for all the nitrate species. The mononitrate species forms the complex of [UO2(H2O)3NO3]+ with a CNeq value of 5, while the di- and trinitrate species have a CNeq value of 6, corresponding to [UO2(H2O)2(NO3)2]0 (D2h) and [UO2(NO3)3]- (D3h), respectively.
Thermodynamic Calculations for Complex Chemical Mixtures
Mcbride, B. J.
1986-01-01
General computer program, CECTRP, developed for calculation of thermodynamic properties of complex mixtures with option to calculate transport properties of these mixtures. Free-energy minimization technique used in equilibrium calculation. Rigorous equations used in transport calculations. Program calculates equilibrium compositions and corresponding thermodynamic and transport properties of mixtures. CECTRP accommodates up to 24 reactants, 20 elements, and 600 products, 400 of which are condensed. Written in FORTRAN IV for any large computer system.
SPECTRAL CALCULATIONS OF HAMILTONIAN FOR A QUANTUM FRACTAL NETWORK
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
A general formulation for the spectral calculations of the Hamiltonian operator of a Quantum Fractal Network(QFN) is presented. The QFN can be constructed by placing artificial neurons on each site of the fractal lattice. An artificial neuron may consist of a cell of a quantum cellular automaton or a quantum dot, which confines a single electron. The Coulomb interaction or the spin-spin interaction between neurons can be used to transmit signals and perform logic operations.The recursive formulas of the eigenvalues and eigenvectors between sub-lattices are obtained explicitly. As the application of the formulations,the eigenvalues and eigenvectors of the Hamiltonian operator for the Sierpinski gasket are calculated.
Efficient wave-function matching approach for quantum transport calculations
DEFF Research Database (Denmark)
Sørensen, Hans Henrik Brandenborg; Hansen, Per Christian; Petersen, Dan Erik;
2009-01-01
The wave-function matching (WFM) technique has recently been developed for the calculation of electronic transport in quantum two-probe systems. In terms of efficiency it is comparable to the widely used Green's function approach. The WFM formalism presented so far requires the evaluation of all ...
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry
Rappoport, Dmitrij; Galvin, Cooper J.; Zubarev, Dmitry; Aspuru-Guzik, Alan
2014-01-01
While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reacti...
Efficient method for the calculation of dissipative quantum transport in quantum cascade lasers.
Greck, Peter; Birner, Stefan; Huber, Bernhard; Vogl, Peter
2015-03-09
We present a novel and very efficient method for calculating quantum transport in quantum cascade lasers (QCLs). It follows the nonequilibrium Green's function (NEGF) framework but sidesteps the calculation of lesser self-energies by replacing them by a quasi-equilibrium expression. This method generalizes the phenomenological Büttiker probe model by taking into account individual scattering mechanisms. It is orders of magnitude more efficient than a fully self-consistent NEGF calculation for realistic devices. We apply this method to a new THz QCL design which works up to 250 K - according to our calculations.
Quantum Chemical Study on Reaction of Acetaldehyde with Hydroxyl Radical
Institute of Scientific and Technical Information of China (English)
LI,Ming(李明); ZHANG,Jin-Sheng(张金生); SHEN,Wei(申伟); MENG,Qing-Xi(孟庆喜)
2004-01-01
The reaction of acetaldehyde with hydroxyl radical was studied by means of quantum chemical methods. The geometries for all the stationary points on the potential energy surfaces were optimized fully, respectively, at the G3MP2, G3, and MP2/6-311++G(d,p) levels. Single-point energies of all the species were calculated at the QCISD/6-311 + +G(d,p) level. The mechanism of the reaction studied was confirmed. The predicted product is acetyl radical that is in agreement with the experiment.
Quantum Matter-Photonics Framework: Analyses of Chemical Conversion Processes
Tapia, O
2014-01-01
A quantum Matter-Photonics framework is adapted to help scrutinize chemical reaction mechanisms and used to explore a process mapped from chemical tree topological model. The chemical concept of bond knitting/breaking is reformulated via partitioned base sets leading to an abstract and general quantum presentation. Pivotal roles are assigned to entanglement, coherence,de-coherence and Feshbach resonance quantum states that permit apprehend gating states in conversion processes. A view from above in the state energy eigenvalue ladder, belonging to full system spectra complement the standard view from ground state. A full quantum physical view supporting chemical change obtains.
Chemical compass for avian magnetoreception as a quantum coherent device
Cai, Jianming
2013-01-01
It is known that more than 50 species use the Earth's magnetic field for orientation and navigation. Intensive studies particularly behavior experiments with birds provide support for a chemical compass based on magnetically sensitive free radical reactions as a source of this sense. However, the fundamental question of whether and how quantum coherence plays an essential role in such a chemical compass model of avian magnetoreception yet remains controversial. Here, we show that the essence of the chemical compass model can be understood in analogy to a quantum interferometer exploiting quantum coherence. Within the framework of quantum metrology, we quantify quantum coherence and demonstrate that it is a resource for chemical magnetoreception. Our results allow us to understand and predict how various factors can affect the performance of a chemical compass from the unique perspective of quantum coherence assisted metrology. This represents a crucial step to affirm avian magnetoreception as an example of qu...
Energy Technology Data Exchange (ETDEWEB)
Kroon, Maaike C. [Physical Chemistry and Molecular Thermodynamics, Department of Chemical Technology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft (Netherlands); Process Equipment, Department of Process and Energy, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft (Netherlands)], E-mail: maaike.kroon@gmail.com; Buijs, Wim [Catalysis Engineering, Department of Chemical Technology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft (Netherlands); Peters, Cor J. [Physical Chemistry and Molecular Thermodynamics, Department of Chemical Technology, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft (Netherlands); Witkamp, Geert-Jan [Process Equipment, Department of Process and Energy, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft (Netherlands)], E-mail: G.J.Witkamp@3me.tudelft.nl
2007-12-15
The long-term thermal stability of ionic liquids is of utmost importance for their industrial application. Although the thermal decomposition temperatures of various ionic liquids have been measured previously, experimental data on the thermal decomposition mechanisms and kinetics are scarce. It is desirable to develop quantitative chemical tools that can predict thermal decomposition mechanisms and temperatures (kinetics) of ionic liquids. In this work ab initio quantum chemical calculations (DFT-B3LYP) have been used to predict thermal decomposition mechanisms, temperatures and the activation energies of the thermal breakdown reactions. These quantum chemical calculations proved to be an excellent method to predict the thermal stability of various ionic liquids.
An extrapolation scheme for solid-state NMR chemical shift calculations
Nakajima, Takahito
2017-06-01
Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.
Computational approach for calculating bound states in quantum field theory
Lv, Q. Z.; Norris, S.; Brennan, R.; Stefanovich, E.; Su, Q.; Grobe, R.
2016-09-01
We propose a nonperturbative approach to calculate bound-state energies and wave functions for quantum field theoretical models. It is based on the direct diagonalization of the corresponding quantum field theoretical Hamiltonian in an effectively discretized and truncated Hilbert space. We illustrate this approach for a Yukawa-like interaction between fermions and bosons in one spatial dimension and show where it agrees with the traditional method based on the potential picture and where it deviates due to recoil and radiative corrections. This method permits us also to obtain some insight into the spatial characteristics of the distribution of the fermions in the ground state, such as the bremsstrahlung-induced widening.
Energy Technology Data Exchange (ETDEWEB)
Minyaev, Ruslan M., E-mail: minyaev@ipoc.sfedu.ru [Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachka Ave., Rostov-on-Don 344090 (Russian Federation); Quapp, Wolfgang; Schmidt, Benjamin [Leipzig University, Mathematical Institute, Augustusplatz, D-04109 Leipzig (Germany); Getmanskii, Ilya V.; Koval, Vitaliy V. [Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachka Ave., Rostov-on-Don 344090 (Russian Federation)
2013-11-08
Highlights: • High level quantum chemical calculations are performed for two S{sub N}2 reactions. • The calculated gradient reaction pathways for reactions have an unusual behavior. • An unusual saddle point of index two lies on the gradient reaction path. • VRI points have been detected by using Newton trajectories for the reaction path. • An infinite flow of gradient lines emanates at three equivalent product minima. - Abstract: Quantum chemical (CCSD(full)/6-311++G(3df,3pd), CCSD(T)(full)/6-311++G(3df,3pd)) and density function theory (B3LYP/6-311++G(3df,3pd)) calculations were performed for the S{sub N}2 nucleophile substitution reactions CH{sub 4} + H{sup −} → CH{sub 4} + H{sup −} and CH{sub 4} + F{sup −} → CH{sub 3}F + H{sup −}. The calculated gradient reaction pathways for both reactions have an unusual behavior. An unusual stationary point of index 2 lies on the gradient reaction path. Using Newton trajectories for the reaction path, we can detect VRI point at which the reaction path branches.
Infinite variance in fermion quantum Monte Carlo calculations.
Shi, Hao; Zhang, Shiwei
2016-03-01
For important classes of many-fermion problems, quantum Monte Carlo (QMC) methods allow exact calculations of ground-state and finite-temperature properties without the sign problem. The list spans condensed matter, nuclear physics, and high-energy physics, including the half-filled repulsive Hubbard model, the spin-balanced atomic Fermi gas, and lattice quantum chromodynamics calculations at zero density with Wilson Fermions, and is growing rapidly as a number of problems have been discovered recently to be free of the sign problem. In these situations, QMC calculations are relied on to provide definitive answers. Their results are instrumental to our ability to understand and compute properties in fundamental models important to multiple subareas in quantum physics. It is shown, however, that the most commonly employed algorithms in such situations have an infinite variance problem. A diverging variance causes the estimated Monte Carlo statistical error bar to be incorrect, which can render the results of the calculation unreliable or meaningless. We discuss how to identify the infinite variance problem. An approach is then proposed to solve the problem. The solution does not require major modifications to standard algorithms, adding a "bridge link" to the imaginary-time path integral. The general idea is applicable to a variety of situations where the infinite variance problem may be present. Illustrative results are presented for the ground state of the Hubbard model at half-filling.
Infinite variance in fermion quantum Monte Carlo calculations
Shi, Hao; Zhang, Shiwei
2016-03-01
For important classes of many-fermion problems, quantum Monte Carlo (QMC) methods allow exact calculations of ground-state and finite-temperature properties without the sign problem. The list spans condensed matter, nuclear physics, and high-energy physics, including the half-filled repulsive Hubbard model, the spin-balanced atomic Fermi gas, and lattice quantum chromodynamics calculations at zero density with Wilson Fermions, and is growing rapidly as a number of problems have been discovered recently to be free of the sign problem. In these situations, QMC calculations are relied on to provide definitive answers. Their results are instrumental to our ability to understand and compute properties in fundamental models important to multiple subareas in quantum physics. It is shown, however, that the most commonly employed algorithms in such situations have an infinite variance problem. A diverging variance causes the estimated Monte Carlo statistical error bar to be incorrect, which can render the results of the calculation unreliable or meaningless. We discuss how to identify the infinite variance problem. An approach is then proposed to solve the problem. The solution does not require major modifications to standard algorithms, adding a "bridge link" to the imaginary-time path integral. The general idea is applicable to a variety of situations where the infinite variance problem may be present. Illustrative results are presented for the ground state of the Hubbard model at half-filling.
Quantum Monte Carlo calculations with chiral effective field theory interactions.
Gezerlis, A; Tews, I; Epelbaum, E; Gandolfi, S; Hebeler, K; Nogga, A; Schwenk, A
2013-07-19
We present the first quantum Monte Carlo (QMC) calculations with chiral effective field theory (EFT) interactions. To achieve this, we remove all sources of nonlocality, which hamper the inclusion in QMC calculations, in nuclear forces to next-to-next-to-leading order. We perform auxiliary-field diffusion Monte Carlo (AFDMC) calculations for the neutron matter energy up to saturation density based on local leading-order, next-to-leading order, and next-to-next-to-leading order nucleon-nucleon interactions. Our results exhibit a systematic order-by-order convergence in chiral EFT and provide nonperturbative benchmarks with theoretical uncertainties. For the softer interactions, perturbative calculations are in excellent agreement with the AFDMC results. This work paves the way for QMC calculations with systematic chiral EFT interactions for nuclei and nuclear matter, for testing the perturbativeness of different orders, and allows for matching to lattice QCD results by varying the pion mass.
From quantum chemical formation free energies to evaporation rates
Directory of Open Access Journals (Sweden)
I. K. Ortega
2012-01-01
Full Text Available Atmospheric new particle formation is an important source of atmospheric aerosols. Large efforts have been made during the past few years to identify which molecules are behind this phenomenon, but the actual birth mechanism of the particles is not yet well known. Quantum chemical calculations have proven to be a powerful tool to gain new insights into the very first steps of particle formation. In the present study we use formation free energies calculated by quantum chemical methods to estimate the evaporation rates of species from sulfuric acid clusters containing ammonia or dimethylamine. We have found that dimethylamine forms much more stable clusters with sulphuric acid than ammonia does. On the other hand, the existence of a very deep local minimum for clusters with two sulfuric acid molecules and two dimethylamine molecules hinders their growth to larger clusters. These results indicate that other compounds may be needed to make clusters grow to larger sizes (containing more than three sulfuric acid molecules.
Calculating Casimir Energies in Renormalizable Quantum Field Theory
Milton, K A
2003-01-01
Quantum vacuum energy has been known to have observable consequences since 1948 when Casimir calculated the force of attraction between parallel uncharged plates, a phenomenon confirmed experimentally with ever increasing precision. Casimir himself suggested that a similar attractive self-stress existed for a conducting spherical shell, but Boyer obtained a repulsive stress. Other geometries and higher dimensions have been considered over the years. Local effects, and divergences associated with surfaces and edges have been considered by several authors. Quite recently, Graham et al. have re-examined such calculations, using conventional techniques of perturbative quantum field theory to remove divergences, and have suggested that previous self-stress results may be suspect. Here we show that the examples considered in their work are misleading; in particular, it is well-known that in two dimensions a circular boundary has a divergence in the Casimir energy for massless fields, while for general dimension $D$...
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.
Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán
2014-03-11
While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.
Remote Chemical Sensing Using Quantum Cascade Lasers
Energy Technology Data Exchange (ETDEWEB)
Harper, Warren W.; Schultz, John F.
2003-01-30
Spectroscopic chemical sensing research at Pacific Northwest National Laboratory (PNNL) is focused on developing advanced sensors for detecting the production of nuclear, chemical, or biological weapons; use of chemical weapons; or the presence of explosives, firearms, narcotics, or other contraband of significance to homeland security in airports, cargo terminals, public buildings, or other sensitive locations. For most of these missions, the signature chemicals are expected to occur in very low concentrations, and in mixture with ambient air or airborne waste streams that contain large numbers of other species that may interfere with spectroscopic detection, or be mistaken for signatures of illicit activity. PNNL’s emphasis is therefore on developing remote and sampling sensors with extreme sensitivity, and resistance to interferents, or selectivity. PNNL’s research activities include: 1. Identification of signature chemicals and quantification of their spectral characteristics, 2. Identification and development of laser and other technologies that enable breakthroughs in sensitivity and selectivity, 3. Development of promising sensing techniques through experimentation and modeling the physical phenomenology and practical engineering limitations affecting their performance, and 4. Development and testing of data collection methods and analysis algorithms. Close coordination of all aspects of the research is important to ensure that all parts are focused on productive avenues of investigation. Close coordination of experimental development and numerical modeling is particularly important because the theoretical component provides understanding and predictive capability, while the experiments validate calculations and ensure that all phenomena and engineering limitations are considered.
Quantum Chemical Study on the Corrosion Inhibition of Some Oxadiazoles
Directory of Open Access Journals (Sweden)
Hong Ju
2015-01-01
Full Text Available Quantum chemical calculations based on DFT method were performed on three nitrogen-bearing heterocyclic compounds used as corrosion inhibitors for the mild steel in acid media to determine the relationship between the molecular structure of inhibitors and inhibition efficiency. The structural parameters, such as energy and distribution of highest occupied molecular orbital (HOMO and lowest unoccupied molecular orbital (LUMO, the charge distribution of the studied inhibitors, the absolute electronegativity (χ values, and the fraction of electrons (ΔN transfer from inhibitors to mild steel were also calculated and correlated with inhibition efficiencies. The results showed that the inhibition efficiency of inhibitors increased with the increase in energy of HOMO and decrease in energy gap of frontier molecular orbital, and the areas containing N and O atoms are most possible sites for bonding the steel surface by donating electrons to the mild steel.
Calculation of the chemical potential in the Gibbs ensemble
Smit, B.; Frenkel, D.
1989-01-01
An expression for the chemical potential in the Gibbs ensemble is derived. For finite system sizes this expression for the chemical potential differs system-atically from Widom's test particle insertion method for the N, V, T ensemble. In order to compare these two methods for calculating the chemic
Quantum-State Controlled Chemical Reactions of Ultracold KRb Molecules
Ospelkaus, S; Wang, D; de Miranda, M H G; Neyenhuis, B; Quéméner, G; Julienne, P S; Bohn, J L; Jin, D S; Ye, J
2009-01-01
How does a chemical reaction proceed at ultralow temperatures? Can simple quantum mechanical rules such as quantum statistics, single scattering partial waves, and quantum threshold laws provide a clear understanding for the molecular reactivity under a vanishing collision energy? Starting with an optically trapped near quantum degenerate gas of polar $^{40}$K$^{87}$Rb molecules prepared in their absolute ground state, we report experimental evidence for exothermic atom-exchange chemical reactions. When these fermionic molecules are prepared in a single quantum state at a temperature of a few hundreds of nanoKelvins, we observe p-wave-dominated quantum threshold collisions arising from tunneling through an angular momentum barrier followed by a near-unity probability short-range chemical reaction. When these molecules are prepared in two different internal states or when molecules and atoms are brought together, the reaction rates are enhanced by a factor of 10 to 100 due to s-wave scattering, which does not ...
Elemike, Elias E.; Nwankwo, Henry U.; Onwudiwe, Damian C.; Hosten, Eric C.
2017-08-01
Two Schiff base compounds with similar backbone, but different positions and lengths of alkyl groups, (E)-4-(((4-propylphenyl)imino)methyl)phenol (PMP) and (E)-4-((2-tolylimino)methyl)phenol (TMP) have been synthesized. Their structures were established by spectroscopic techniques which include FTIR, 1H and 13C NMR, relative molecular mass (mass spect.), and single crystal X-ray crystallography. The spectroscopic methods revealed the characteristic imine functional groups and the exact molecular masses of the compounds. Single crystal analysis revealed an orthorhombic crystal system with Pca21 space group for the two compounds; and the structure of PMP reveal that the propyl group is disordered over two positions in 0.79:0.21 ratio. The corrosion inhibition behaviour of the two Schiff bases were studied by electrochemical measurements. The results suggest that the two derivatives adsorbed onto the mild steel surface and formed hydrophobic films, which to an appreciable extent, protected the surface of the mild steel. Potentiodynamic polarization results strongly suggested that the investigated Schiff bases behave as mixed-type inhibitors with a more pronounced cathodic nature, and the adsorption isotherm basically obeys the Langmuir isotherm. Quantum chemical computations were also employed to provide further explanations on the adsorption mode, and the theoretical predictions conformed to the experimental results.
Quantum chemical study on the corrosion inhibition property of some heterocyclic azole derivatives
Directory of Open Access Journals (Sweden)
N. Anusuya
2015-09-01
Full Text Available Quantum chemical calculations based on density functional theory (DFT method were performed on heterocyclic azole derivatives as corrosion inhibitors for mild steel in acid media to investigate the relationship between molecular structure of the inhibitors and the corresponding inhibition efficiencies (%. Quantum chemical parameters most relevant to their potential action as corrosion inhibitors have been calculated in the non-protonated and protonated forms in aqueous phase for comparison. Results obtained in this study indicate thatin acidic media, both the protonated and non-protonated forms of the azoles represent the better actual experimental situation.
Institute of Scientific and Technical Information of China (English)
Liu Yu-Min; Yu Zhong-Yuan
2009-01-01
Calculations of electronic structures about the semiconductor quantum dot and the semiconductor quantum ring are presented in this paper. To reduce the calculation costs, for the quantum dot and the quantum ring, their simplified axially symmetric shapes are utilized in our analysis. The energy dependent effective mass is taken into account in solving the Schrodinger equations in the single band effective mass approximation. The calculated results show that the energy dependent effective mass should be considered only for relatively small volume quantum dots or small quantum rings. For large size quantum materials, both the energy dependent effective mass and the parabolic effective mass can give the same results. The energy states and the effective masses of the quantum dot and the quantum ring as a function of geometric parameters are also discussed in detail.
Institute of Scientific and Technical Information of China (English)
LI Chang-Hong; LI Wei; LI Yu-Lin; YANG Ying-Qun
2012-01-01
A three-dimensional framework copper（Ⅱ） coordination polymer with copper carbonate basic and 3-（pyridin-2-yl）-1,2,4-triazole （Hpt） has been hydrothemally synthesized.The complex （2,C14 H10 CuN8 ·3H2 O） crystallizes in tetragonal,space group P4 2 /n,a=2.08581（12）,b=2.08581（12）,c=0.72331（4） nm,M r=761.73,V=3.1468（3） nm 3,Dc=1.608 g/cm 3,Z=4,F（000）=1552,GOOF=1.07,R=0.0515 and wR=0.1689.Every asymmetric unit molecular structure of the complex is composed with one copper ion,one and half water molecules and two Hpt molecules.Each copper ion is coordinated with five nitrogen atoms from four Hpt molecules,forming a distorted square pyramidal geometry.The fluorescence spectrum analysis shows that the title complex at room temperature exhibits intense photoluminescence with maximum emission at 450 nm.The quantum chemistry calculation study on the complex has been performed.The stability,some frontier molecular orbital energies and composition characteristics of some frontier molecular orbitals of the complex have been investigated.
Precision decay rate calculations in quantum field theory
Andreassen, Anders; Frost, William; Schwartz, Matthew D
2016-01-01
Tunneling in quantum field theory is worth understanding properly, not least because it controls the long term fate of our universe. There are however, a number of features of tunneling rate calculations which lack a desirable transparency, such as the necessity of analytic continuation, the appropriateness of using an effective instead of classical potential, and the sensitivity to short-distance physics. This paper attempts to review in pedagogical detail the physical origin of tunneling and its connection to the path integral. Both the traditional potential-deformation method and a recent more direct propagator-based method are discussed. Some new insights from using approximate semi-classical solutions are presented. In addition, we explore the sensitivity of the lifetime of our universe to short distance physics, such as quantum gravity, emphasizing a number of important subtleties.
Calculation of hyperfine interaction in spherical quantum dot
Yakar, Yusuf; Çakır, Bekir; Özmen, Ayhan
2015-10-01
In this study, we have calculated the unperturbed wavefunctions and energy eigenvalues of the ground and excited states of a spherical quantum dot, GaAs/AlxGa1-xAs, by using quantum genetic algorithm and Hartree-Fock Roothaan method. Hyperfine coupling constant and hyperfine energy of 1s, 2p, 3d and 4f levels are carried out as a function of dot radius. The results show that the hyperfine constant and hyperfine energy varies rapidly in the strong and medium confining regions as dot radius decreases. It is worth pointing out that dot radius, impurity charge and angular momentum have a strong influence on the hyperfine energy. It is also found that hyperfine energy and hyperfine splitting vary with aluminium concentration ratio x.
Delay time calculation for dual-wavelength quantum cascade lasers
Energy Technology Data Exchange (ETDEWEB)
Hamadou, A., E-mail: abd-hamado@yahoo.fr [Département des Sciences et Techniques, Faculté des Sciences et de la Technologie, Université de Bordj Bou Arreridj 34000 (Algeria); Laboratoire d’étude des surfaces et interfaces des matériaux solides (LESIMS), Sétif 19000 (Algeria); Lamari, S. [Laboratoire d’étude des surfaces et interfaces des matériaux solides (LESIMS), Sétif 19000 (Algeria); Département de Physique, Faculté des Sciences, Université Sétif 1, 19000 (Algeria); Thobel, J.-L. [Institut d' Electronique, de Microélectronique et de Nanotechnologie (IEMN), UMR 8520, Université Lille1, Avenue Poincaré, BP 60069, 59652 Villeneuve d' Ascq Cédex (France)
2013-11-28
In this paper, we calculate the turn-on delay (t{sub th}) and buildup (Δt) times of a midinfrared quantum cascade laser operating simultaneously on two laser lines having a common upper level. The approach is based on the four-level rate equations model describing the variation of the electron number in the states and the photon number present within the cavity. We obtain simple analytical formulae for the turn-on delay and buildup times that determine the delay times and numerically apply our results to both the single and bimode states of a quantum cascade laser, in addition the effects of current injection on t{sub th} and Δt are explored.
Calculation and Improvement on External Quantum Efficiency of OLEDs
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
The calculation of the external quantum efficiency(ηext) of organic light-emitting devices(OLEDs) is presented theoretically. The basic idea is to obtain ηext by calculating the fraction of the generated light that can escape through the top surface and the average transmittance over the escape cone. During the calculation, the effects of the interference, absorption and multiple reflections are neglected. Then a result of a typical 8-tris-hydroxyquinoline aluminum(Alq3)-based OLEDs on a planar glass substrate is obtained. And a twice increase in ηext can be achieved by using a high-index-glass substrate with an antireflection coating(SiO2) on substrate surface.
Chemical accuracy from quantum Monte Carlo for the Benzene Dimer
Azadi, Sam
2015-01-01
We report an accurate study of interactions between Benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory (DFT) using different van der Waals (vdW) functionals. In our QMC calculations, we use accurate correlated trial wave functions including three-body Jastrow factors, and backflow transformations. We consider two benzene molecules in the parallel displaced (PD) geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the CCSD(T)/CBS limit is -2.65(2) kcal/mol [E. Miliordos et al, J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, compar...
Energy Technology Data Exchange (ETDEWEB)
Tucker, Jon R.; Magyar, Rudolph J.
2012-02-01
High explosives are an important class of energetic materials used in many weapons applications. Even with modern computers, the simulation of the dynamic chemical reactions and energy release is exceedingly challenging. While the scale of the detonation process may be macroscopic, the dynamic bond breaking responsible for the explosive release of energy is fundamentally quantum mechanical. Thus, any method that does not adequately describe bonding is destined to lack predictive capability on some level. Performing quantum mechanics calculations on systems with more than dozens of atoms is a gargantuan task, and severe approximation schemes must be employed in practical calculations. We have developed and tested a divide and conquer (DnC) scheme to obtain total energies, forces, and harmonic frequencies within semi-empirical quantum mechanics. The method is intended as an approximate but faster solution to the full problem and is possible due to the sparsity of the density matrix in many applications. The resulting total energy calculation scales linearly as the number of subsystems, and the method provides a path-forward to quantum mechanical simulations of millions of atoms.
Radiation and quantum chemical studies of chalcone derivatives.
Gaikwad, P; Priyadarsini, K I; Naumov, S; Rao, B S M
2010-08-05
The reactions of oxidizing radicals ((*)OH, Br(2)(*-), and SO(4)(*-)) with -OH-, -CH(3)-, or -NH(2)-substituted indole chalcones and hydroxy benzenoid chalcones were studied by radiation and quantum chemical methods. The (*)OH radical was found to react by addition at diffusion-controlled rates (k = 1.1-1.7 x 10(10) dm(3) mol(-1) s(-1)), but Br(2)(*-) radical reacted by 2 orders of magnitude lower. Quantum chemical calculations at the B3LYP/6-31+G(d,p) level of theory have shown that the (C2-OH)(*), (C11-OH)(*), and (C10-OH)(*) adducts of the indole chalcones and the (C7-OH)(*) and (C8-OH)(*) adducts of the hydroxy benzenoid chalcones are more stable with DeltaH = -39 to -28 kcal mol(-1) and DeltaG = -32 to -19 kcal mol(-1). This suggests that (*)OH addition to the alpha,beta-unsaturated bond is a major reaction channel in both types of chalcones and is barrierless. The stability and lack of dehydration of the (*)OH adducts arise from two factors: strong frontier orbital interaction due to the low energy gap between interacting orbitals and the negligible Coulombic repulsion due to small absolute values of Mulliken charges. The transient absorption spectrum measured in the (*)OH radical reaction with all the indole chalcone derivatives exhibited a maximum at 390 nm, which is in excellent agreement with the computed value (394 nm). The formation of three phenolic products under steady-state radiolysis is in line with the three stable (*)OH adducts predicted by theory. Independent of the substituent, identical spectra (lambda(max) = 330-360 and approximately 580 nm) were obtained on one-electron oxidation of the three indole chalcones. MO calculations predict the deprotonation from the -NH group is more efficient than from the substituent due to the larger electron density on the N1 atom forming the chalcone indolyl radical. Its reduction potential was determined to be 0.56 V from the ABTS(*-)/ABTS(2-) couple. In benzenoid chalcones, the (*)OH adduct spectrum is
Infinite Variance in Fermion Quantum Monte Carlo Calculations
Shi, Hao
2015-01-01
For important classes of many-fermion problems, quantum Monte Carlo (QMC) methods allow exact calculations of ground-state and finite-temperature properties, without the sign problem. The list spans condensed matter, nuclear physics, and high-energy physics, including the half-filled repulsive Hubbard model, the spin-balanced atomic Fermi gas, lattice QCD calculations at zero density with Wilson Fermions, and is growing rapidly as a number of problems have been discovered recently to be free of the sign problem. In these situations, QMC calculations are relied upon to provide definitive answers. Their results are instrumental to our ability to understand and compute properties in fundamental models important to multiple sub-areas in quantum physics. It is shown, however, that the most commonly employed algorithms in such situations turn out to have an infinite variance problem. A diverging variance causes the estimated Monte Carlo statistical error bar to be incorrect, which can render the results of the calc...
An Emphasis of Electron Energy Calculation in Quantum Wells
Institute of Scientific and Technical Information of China (English)
GAOShao-Wen; CAOJun-Cheng; FENGSong-Lin
2004-01-01
We investigate various methods for the calculation of the electron energy in semiconductor quantum wells and focus on a matrix algorithm method. The results show better fitness of the factor -h2/2 э/эz 1/m*（z） э/эz than that of -h2/2 1/m*（z） э2/эz2 in the first part of the Schroedinger equation. The effect of nonparabolicity in the conduction band is also discussed.
Importance of parametrizing constraints in quantum-mechanical variational calculations
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.
Calculation of exchange interaction for modified Gaussian coupled quantum dots
Khordad, R.
2017-08-01
A system of two laterally coupled quantum dots with modified Gaussian potential has been considered. Each quantum dot has an electron under electric and magnetic field. The quantum dots have been considered as hydrogen-like atoms. The physical picture has translated into the Heisenberg spin Hamiltonian. The Schrödinger equation using finite element method has been numerically solved. The exchange energy factor has been calculated as a functions of electric field, magnetic field, and the separation distance between the centers of the dots ( d). According to the results, it is found that there is the transition from anti-ferromagnetic to ferromagnetic for constant electric field. Also, the transition occurs from ferromagnetic to anti-ferromagnetic for constant magnetic field (B>1 T). With decreasing the distance between the centers of the dots and increasing magnetic field, the transition occurs from anti-ferromagnetic to ferromagnetic. It is found that a switching of exchange energy factor is presented without canceling the interactions of the electric and magnetic fields on the system.
Chemically mediated quantum criticality in NbFe2.
Alam, Aftab; Johnson, D D
2011-11-11
Laves-phase Nb(1+c)Fe(2-c) is a rare itinerant intermetallic compound exhibiting magnetic quantum criticality at c(cr)∼1.5%Nb excess; its origin, and how alloying mediates it, remains an enigma. For NbFe(2), we show that an unconventional band critical point above the Fermi level E(F) explains most observations and that chemical alloying mediates access to this unconventional band critical point by an increase in E(F) with decreasing electrons (increasing %Nb), counter to rigid-band concepts. We calculate that E(F) enters the unconventional band critical point region for c(cr) > 1.5%Nb and by 1.74%Nb there is no Nb site-occupation preference between symmetry-distinct Fe sites, i.e., no electron-hopping disorder, making resistivity near constant as observed. At larger Nb (Fe) excess, the ferromagnetic Stoner criterion is satisfied.
Chemical potential and compressibility of quantum Hall bilayer excitons,.
Energy Technology Data Exchange (ETDEWEB)
Skinner, Brian
2016-02-25
I consider a system of two parallel quantum Hall layers with total filling factor 0 or 1. When the distance between the layers is small enough, electrons and holes in opposite layers can form inter-layer excitons, which have a finite effective mass and interact via a dipole-dipole potential. I present results for the chemical potential u of the resulting bosonic system as a function of the exciton concentration n and the interlayer separation d. I show that both u and the interlayer capacitance have an unusual nonmonotonic dependence on d, owing to the interplay between an increasing dipole moment and an increasing effective mass with increasing d. Finally, I discuss the transition between the superfluid and Wigner crystal phases, which is shown to occur at d x n-1/10. Results are derived first via simple intuitive arguments, and then verified with more careful analytic derivations and numeric calculations.
USI/Chemplex/Quantum Chemical Co. Outfall Study, 1987
US Fish and Wildlife Service, Department of the Interior — Sediment samples collected in 1987 from the Quantum Chemical Corporation outfall on the Upper Mississippi River detected 14 polycyclic aromatic hydrocarbons (PAH's)....
Accelerating atomistic calculations of quantum energy eigenstates on graphic cards
Rodrigues, Walter; Pecchia, A.; Lopez, M.; Auf der Maur, M.; Di Carlo, A.
2014-10-01
Electronic properties of nanoscale materials require the calculation of eigenvalues and eigenvectors of large matrices. This bottleneck can be overcome by parallel computing techniques or the introduction of faster algorithms. In this paper we report a custom implementation of the Lanczos algorithm with simple restart, optimized for graphical processing units (GPUs). The whole algorithm has been developed using CUDA and runs entirely on the GPU, with a specialized implementation that spares memory and reduces at most machine-to-device data transfers. Furthermore parallel distribution over several GPUs has been attained using the standard message passing interface (MPI). Benchmark calculations performed on a GaN/AlGaN wurtzite quantum dot with up to 600,000 atoms are presented. The empirical tight-binding (ETB) model with an sp3d5s∗+spin-orbit parametrization has been used to build the system Hamiltonian (H).
Quantum Monte Carlo Calculations of Nucleon-Nucleus Scattering
Wiringa, R. B.; Nollett, Kenneth M.; Pieper, Steven C.; Brida, I.
2009-10-01
We report recent quantum Monte Carlo (variational and Green's function) calculations of elastic nucleon-nucleus scattering. We are adding the cases of proton-^4He, neutron-^3H and proton-^3He scattering to a previous GFMC study of neutron-^4He scattering [1]. To do this requires generalizing our methods to include long-range Coulomb forces and to treat coupled channels. The two four-body cases can be compared to other accurate four-body calculational methods such as the AGS equations and hyperspherical harmonic expansions. We will present results for the Argonne v18 interaction alone and with Urbana and Illinois three-nucleon potentials. [4pt] [1] K.M. Nollett, S. C. Pieper, R.B. Wiringa, J. Carlson, and G.M. Hale, Phys. Rev. Lett. 99, 022502 (2007)
Automated quantum conductance calculations using maximally-localised Wannier functions
Shelley, Matthew; Mostofi, Arash A; Marzari, Nicola
2011-01-01
A robust, user-friendly, and automated method to determine quantum conductance in disordered quasi-one-dimensional systems is presented. The scheme relies upon an initial density- functional theory calculation in a specific geometry after which the ground-state eigenfunctions are transformed to a maximally-localised Wannier function (MLWF) basis. In this basis, our novel algorithms manipulate and partition the Hamiltonian for the calculation of coherent electronic transport properties within the Landauer-Buttiker formalism. Furthermore, we describe how short- ranged Hamiltonians in the MLWF basis can be combined to build model Hamiltonians of large (>10,000 atom) disordered systems without loss of accuracy. These automated algorithms have been implemented in the Wannier90 code[Mostofi et al, Comput. Phys. Commun. 178, 685 (2008)], which is interfaced to a number of electronic structure codes such as Quantum-ESPRESSO, AbInit, Wien2k, SIESTA and FLEUR. We apply our methods to an Al atomic chain with a Na defect...
Carbon Footprint Calculations: An Application of Chemical Principles
Treptow, Richard S.
2010-01-01
Topics commonly taught in a general chemistry course can be used to calculate the quantity of carbon dioxide emitted into the atmosphere by various human activities. Each calculation begins with the balanced chemical equation for the reaction that produces the CO[subscript 2] gas. Stoichiometry, thermochemistry, the ideal gas law, and dimensional…
Chemical Bond Calculations of Crystal Growth of KDP and ADP
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
A novel method was proposed to calculate the crystal morphology (or growth habit) on the basis of chemical bond analysis. All constituent chemical bonds were distinguished as relevant and independent bonds according to their variations during the crystallization process. By employing the current method, the influence of specific growth conditions on the crystal morphology can be considered in the structure analysis process. The ideal morphologies of both KDP (KH2PO4) and ADP (NH4H2PO4) crystals were calculated and compared with our obtained crystallites at room temperature, which validates the present calculation method very well.
QmeQ 1.0: An open-source Python package for calculations of transport through quantum dot devices
DEFF Research Database (Denmark)
Kiršanskas, Gediminas; Pedersen, Jonas Nyvold; Karlström, Olov
2017-01-01
QmeQ is an open-source Python package for numerical modeling of transport through quantum dot devices with strong electron–electron interactions using various approximate master equation approaches. The package provides a framework for calculating stationary particle or energy currents driven...... by differences in chemical potentials or temperatures between the leads which are tunnel coupled to the quantum dots. The electronic structures of the quantum dots are described by their single-particle states and the Coulomb matrix elements between the states. When transport is treated perturbatively to lowest...
Gangarapu, S.; Marcelis, A.T.M.; Zuilhof, H.
2013-01-01
The influence of electronic and steric effects on the stabilities of carbamates formed from the reaction of CO2 with a wide range of alkanolamines was investigated by quantum chemical methods. For the calculations, B3LYP, M11-L, MP2, and spin-component-scaled MP2 (SCS-MP2) methods were used, coupled
Zuilhof, H.; Morokuma, K.
2003-01-01
Quantum chemical calculations were used to rationalize the observed enantiodifferentiation in the complexation of alpha-amino acids to chiral Cu(II) complexes. Apart from Cu(II)-pi interactions and steric repulsions between the anchoring cholesteryl-Glu moiety and an aromatic amino acid R group, hyd
Gangarapu, S.; Marcelis, A.T.M.; Zuilhof, H.
2013-01-01
The influence of electronic and steric effects on the stabilities of carbamates formed from the reaction of CO2 with a wide range of alkanolamines was investigated by quantum chemical methods. For the calculations, B3LYP, M11-L, MP2, and spin-component-scaled MP2 (SCS-MP2) methods were used, coupled
DEFF Research Database (Denmark)
Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;
2013-01-01
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...
Characterization of heterocyclic rings through quantum chemical topology.
Griffiths, Mark Z; Popelier, Paul L A
2013-07-22
Five-membered rings are found in a myriad of molecules important in a wide range of areas such as catalysis, nutrition, and drug and agrochemical design. Systematic insight into their largely unexplored chemical space benefits from first principle calculations presented here. This study comprehensively investigates a grand total of 764 different rings, all geometry optimized at the B3LYP/6-311+G(2d,p) level, from the perspective of Quantum Chemical Topology (QCT). For the first time, a 3D space of local topological properties was introduced, in order to characterize rings compactly. This space is called RCP space, after the so-called ring critical point. This space is analogous to BCP space, named after the bond critical point, which compactly and successfully characterizes a chemical bond. The relative positions of the rings in RCP space are determined by the nature of the ring scaffold, such as the heteroatoms within the ring or the number of π-bonds. The summed atomic QCT charges of the five ring atoms revealed five features (number and type of heteroatom, number of π-bonds, substituent and substitution site) that dictate a ring's net charge. Each feature independently contributes toward a ring's net charge. Each substituent has its own distinct and systematic effect on the ring's net charge, irrespective of the ring scaffold. Therefore, this work proves the possibility of designing a ring with specific properties by fine-tuning it through manipulation of these five features.
Energy Technology Data Exchange (ETDEWEB)
Schmidt, M.W.
1982-12-01
The Full Optimized Reaction Space (FORS) model is used for the theoretical calculation of molecular potential energy surfaces involved in chemical reactions. The FORS model is applied to two polyatomic reactions: the dihydrogen exchange between ethane and etylene, and the formation and dissolution of dioxirane and dioxymethane. The former reaction is found to possess a high barrier, in spite of its symmetry allowed nature. The latter reaction involves significant configuration mixing as methylene and oxygen react to form, successively, dioxirane, dioxymethane, and hydrogen and carbon dioxide. Finally, FORS wavefunctions can be expressed in terms of a basis of antisymmetrized products of atomic state functions, using the predominantly atomic projected localized orbitals. The atoms in molecules analysis permits the incorporation of data from atomic spectra into the molecular Hamiltonian to achieve the IntraAtomic Correlation Correction (IACC). The IACC scheme is illustrated for a few small diatomics (H/sub 2/, NH, F/sub 2/), and is shown to yield more accurate results than the uncorrected FORS wavefunctions.
Parveen, Shana; Al-Alshaikh, Monirah A.; Panicker, C. Yohannan; El-Emam, Ali A.; Salian, Vinutha V.; Narayana, B.; Sarojini, B. K.; van Alsenoy, C.
2016-09-01
In this work, the vibrational spectral analysis was carried out using FT-IR and FT-Raman spectroscopy of (2E)-1-(4-Chlorophenyl)-3-[4-(propan-2-yl)phenyl]prop-2-en-1-one. The computations were performed at DFT level of theory to get the optimizedgeometry and vibrational wave numbers of the normal modes of the title compound using Gaussian09 software. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution. The calculated HOMO and LUMO energies show chemical activity of the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The hyperpolarizability values are reported and the first hyperpolarizability of the title compound is 83.85 times that of standard NLO material urea. From the MEP plot, the negative electrostatic potential regions are mainly localized over the carbonyl group, the phenyl rings and are possible sites for electrophilic attack. The positive regions are localized over all the hydrogen atoms and are possible sites for nucleophilic attack. The molecular docking results suggest that the compound might exhibit inhibitory activity against lymphocyte-specific kinase and may results in design of novel T-cell immunosuppressants.
Quantum-chemical insights from deep tensor neural networks
Schütt, Kristof T.; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R.; Tkatchenko, Alexandre
2017-01-01
Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol-1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.
Quantum Monte Carlo Calculations Applied to Magnetic Molecules
Energy Technology Data Exchange (ETDEWEB)
Engelhardt, Larry [Iowa State Univ., Ames, IA (United States)
2006-01-01
We have calculated the equilibrium thermodynamic properties of Heisenberg spin systems using a quantum Monte Carlo (QMC) method. We have used some of these systems as models to describe recently synthesized magnetic molecules, and-upon comparing the results of these calculations with experimental data-have obtained accurate estimates for the basic parameters of these models. We have also performed calculations for other systems that are of more general interest, being relevant both for existing experimental data and for future experiments. Utilizing the concept of importance sampling, these calculations can be carried out in an arbitrarily large quantum Hilbert space, while still avoiding any approximations that would introduce systematic errors. The only errors are statistical in nature, and as such, their magnitudes are accurately estimated during the course of a simulation. Frustrated spin systems present a major challenge to the QMC method, nevertheless, in many instances progress can be made. In this chapter, the field of magnetic molecules is introduced, paying particular attention to the characteristics that distinguish magnetic molecules from other systems that are studied in condensed matter physics. We briefly outline the typical path by which we learn about magnetic molecules, which requires a close relationship between experiments and theoretical calculations. The typical experiments are introduced here, while the theoretical methods are discussed in the next chapter. Each of these theoretical methods has a considerable limitation, also described in Chapter 2, which together serve to motivate the present work. As is shown throughout the later chapters, the present QMC method is often able to provide useful information where other methods fail. In Chapter 3, the use of Monte Carlo methods in statistical physics is reviewed, building up the fundamental ideas that are necessary in order to understand the method that has been used in this work. With these
Quantum-chemical approach to defect formation processes in non-metallic crystals
Energy Technology Data Exchange (ETDEWEB)
Kotomin, E.A.; Shluger, A.L. (Latvijskij Gosudarstvennyj Univ., Riga (USSR))
1989-01-01
Results of the quantum-chemical simulation of the formation of structural and radiation defects are reviewed, using ice, silicon, and silicon dioxide as examples. The relationship between the structural elements of these crystals and the structural defects is analysed. Models of the main defects, their optical characteristics, and the activation energy of their migration are discussed. The relationship between the characteristics obtained by quantum-chemical calculations and the parameters of the macroscopic kinetics of the processes induced by defects in dielectric crystals is considered. (author).
Quantum Monte Carlo calculations with chiral effective field theory interactions
Energy Technology Data Exchange (ETDEWEB)
Tews, Ingo
2015-10-12
The neutron-matter equation of state connects several physical systems over a wide density range, from cold atomic gases in the unitary limit at low densities, to neutron-rich nuclei at intermediate densities, up to neutron stars which reach supranuclear densities in their core. An accurate description of the neutron-matter equation of state is therefore crucial to describe these systems. To calculate the neutron-matter equation of state reliably, precise many-body methods in combination with a systematic theory for nuclear forces are needed. Chiral effective field theory (EFT) is such a theory. It provides a systematic framework for the description of low-energy hadronic interactions and enables calculations with controlled theoretical uncertainties. Chiral EFT makes use of a momentum-space expansion of nuclear forces based on the symmetries of Quantum Chromodynamics, which is the fundamental theory of strong interactions. In chiral EFT, the description of nuclear forces can be systematically improved by going to higher orders in the chiral expansion. On the other hand, continuum Quantum Monte Carlo (QMC) methods are among the most precise many-body methods available to study strongly interacting systems at finite densities. They treat the Schroedinger equation as a diffusion equation in imaginary time and project out the ground-state wave function of the system starting from a trial wave function by propagating the system in imaginary time. To perform this propagation, continuum QMC methods require as input local interactions. However, chiral EFT, which is naturally formulated in momentum space, contains several sources of nonlocality. In this Thesis, we show how to construct local chiral two-nucleon (NN) and three-nucleon (3N) interactions and discuss results of first QMC calculations for pure neutron systems. We have performed systematic auxiliary-field diffusion Monte Carlo (AFDMC) calculations for neutron matter using local chiral NN interactions. By
Using the Chebychev expansion in quantum transport calculations
Energy Technology Data Exchange (ETDEWEB)
Popescu, Bogdan; Rahman, Hasan; Kleinekathöfer, Ulrich, E-mail: u.kleinekathoefer@jacobs-university.de [Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen (Germany)
2015-04-21
Irradiation by laser pulses and a fluctuating surrounding liquid environment can, for example, lead to time-dependent effects in the transport through molecular junctions. From the theoretical point of view, time-dependent theories of quantum transport are still challenging. In one of these existing transport theories, the energy-dependent coupling between molecule and leads is decomposed into Lorentzian functions. This trick has successfully been combined with quantum master approaches, hierarchical formalisms, and non-equilibrium Green’s functions. The drawback of this approach is, however, its serious limitation to certain forms of the molecule-lead coupling and to higher temperatures. Tian and Chen [J. Chem. Phys. 137, 204114 (2012)] recently employed a Chebychev expansion to circumvent some of these latter problems. Here, we report on a similar approach also based on the Chebychev expansion but leading to a different set of coupled differential equations using the fact that a derivative of a zeroth-order Bessel function can again be given in terms of Bessel functions. Test calculations show the excellent numerical accuracy and stability of the presented formalism. The time span for which this Chebychev expansion scheme is valid without any restrictions on the form of the spectral density or temperature can be determined a priori.
Using the Chebychev expansion in quantum transport calculations.
Popescu, Bogdan; Rahman, Hasan; Kleinekathöfer, Ulrich
2015-04-21
Irradiation by laser pulses and a fluctuating surrounding liquid environment can, for example, lead to time-dependent effects in the transport through molecular junctions. From the theoretical point of view, time-dependent theories of quantum transport are still challenging. In one of these existing transport theories, the energy-dependent coupling between molecule and leads is decomposed into Lorentzian functions. This trick has successfully been combined with quantum master approaches, hierarchical formalisms, and non-equilibrium Green's functions. The drawback of this approach is, however, its serious limitation to certain forms of the molecule-lead coupling and to higher temperatures. Tian and Chen [J. Chem. Phys. 137, 204114 (2012)] recently employed a Chebychev expansion to circumvent some of these latter problems. Here, we report on a similar approach also based on the Chebychev expansion but leading to a different set of coupled differential equations using the fact that a derivative of a zeroth-order Bessel function can again be given in terms of Bessel functions. Test calculations show the excellent numerical accuracy and stability of the presented formalism. The time span for which this Chebychev expansion scheme is valid without any restrictions on the form of the spectral density or temperature can be determined a priori.
Matrix product state calculations for one-dimensional quantum chains and quantum impurity models
Energy Technology Data Exchange (ETDEWEB)
Muender, Wolfgang
2011-09-28
involving a Kondo exciton and population switching in quantum dots. It turns out that both phenomena rely on the various manifestations of Anderson orthogonality (AO), which describes the fact that the response of the Fermi sea to a quantum quench (i.e. an abrupt change of some property of the impurity or quantum dot) is a change of the scattering phase shifts of all the single-particle wave functions, therefore drastically changing the system. In this context, we demonstrate that NRG, a highly accurate method for quantum impurity models, allows for the calculation of all static and dynamic quantities related to AO and present an extensive NRG study for population switching in quantum dots. (orig.)
Quantum-Mechanical Calculations on Molecular Substructures Involved in Nanosystems
Directory of Open Access Journals (Sweden)
Beata Szefler
2014-09-01
Full Text Available In this review article, four ideas are discussed: (a aromaticity of fullerenes patched with flowers of 6-and 8-membered rings, optimized at the HF and DFT levels of theory, in terms of HOMA and NICS criteria; (b polybenzene networks, from construction to energetic and vibrational spectra computations; (c quantum-mechanical calculations on the repeat units of various P-type crystal networks and (d construction and stability evaluation, at DFTB level of theory, of some exotic allotropes of diamond D5, involved in hyper-graphenes. The overall conclusion was that several of the yet hypothetical molecular nanostructures herein described are serious candidates to the status of real molecules.
Quantum plasmonics: from jellium models to ab initio calculations
Directory of Open Access Journals (Sweden)
Varas Alejandro
2016-08-01
Full Text Available Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
Conformational analysis of small molecules: NMR and quantum mechanics calculations.
Tormena, Cláudio F
2016-08-01
This review deals with conformational analysis in small organic molecules, and describes the stereoelectronic interactions responsible for conformational stability. Conformational analysis is usually performed using NMR spectroscopy through measurement of coupling constants at room or low temperature in different solvents to determine the populations of conformers in solution. Quantum mechanical calculations are used to address the interactions responsible for conformer stability. The conformational analysis of a large number of small molecules is described, using coupling constant measurements in different solvents and at low temperature, as well as recent applications of through-space and through-hydrogen bond coupling constants JFH as tools for the conformational analysis of fluorinated molecules. Besides NMR parameters, stereoelectronic interactions such as conjugative, hyperconjugative, steric and intramolecular hydrogen bond interactions involved in conformational preferences are discussed.
Calculations of proton chemical shifts in olefins and aromatics
Escrihuela, M C
2000-01-01
induced reagents on alpha,beta unsaturated ketones has also been investigated in order to deduce molecular structures and to obtain the assignment of the spectra of these molecules. A semi-empirical calculation of the partial atomic charges in organic compounds based on molecular dipole moments (CHARGE3) was developed into a model capable of predicting proton chemical shifts in a wide variety of organic compounds to a reasonable degree of accuracy. The model has been modified to include condensed aromatic hydrocarbons and substituted benzenes, alkenes, halo-monosubstituted benzenes and halo-alkenes. Within the aromatic compounds the influence of the pi electron densities and the ring current have been investigated, along with the alpha, beta and gamma effects. The model gives the first accurate calculation of the proton chemical shifts of condensed aromatic compounds and the proton substituent chemical shifts (SCS) in the benzene ring. For the data set of 55 proton chemical shifts spanning 3 ppm the rms error...
Spectroscopic and quantum chemical analysis of Isonicotinic acid methyl ester
Shoba, D.; Periandy, S.; Govindarajan, M.; Gayathri, P.
2015-02-01
In this present study, an organic compound Isonicotinic acid methyl ester (INAME) was structurally characterized by FTIR, FT-Raman, and NMR and UV spectroscopy. The optimized geometrical parameters and energies of all different and possible conformers of INAME are obtained from Density Functional Theory (DFT) by B3LYP/6-311++G(d,p) method. There are three conformers (SI, SII-1, and SII-2) for this molecule (ground state). The most stable conformer of INAME is SI conformer. The molecular geometry and vibrational frequencies of INAME in the ground state have been calculated by using HF and density functional method (B3LYP) 6-311++G (d,p) basis set. Detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The computed vibrational frequencies were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. A study on the electronic properties, such as HOMO and LUMO energies were performed by time independent DFT approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and first hyper polarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results show that the INAME molecule may have microscopic nonlinear optical (NLO) behavior with non zero values. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by gauge independent atomic orbital (GIAO) method.
Mazurek, A. P.; Sadlej-Sosnowska, N.
2000-11-01
A comparison of the ab initio quantum chemical methods: Hartree-Fock (HF) and hybrid density functional theory (DFT)/B3LYP for the treatment of tautomeric equilibria both in the gas phase and in the solution is made. The solvent effects were investigated in terms of the self-consistent reaction field (SCRF). Ionization potentials (IP), calculated by DFT/B3LYP, are also compared with those calculated previously within the HF frame.
Chemical potential calculations in dense liquids using metadynamics
Perego, C.; Giberti, F.; Parrinello, M.
2016-10-01
The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.
Chemical Potential Calculations In Dense Liquids Using Metadynamics
Perego, Claudio; Parrinello, Michele
2016-01-01
The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.
Sequential Voronoi diagram calculations using simple chemical reactions
Costello, Ben de Lacy; Adamatzky, Andy
2012-01-01
In our recent paper [de Lacy Costello et al. 2010] we described the formation of complex tessellations of the plane arising from the various reactions of metal salts with potassium ferricyanide and ferrocyanide loaded gels. In addition to producing colourful tessellations these reactions are naturally computing generalised Voronoi diagrams of the plane. The reactions reported previously were capable of the calculation of three distinct Voronoi diagrams of the plane. As diffusion coupled with a chemical reaction is responsible for the calculation then this is achieved in parallel. Thus an increase in the complexity of the data input does not utilise additional computational resource. Additional benefits of these chemical reactions is that a permanent record of the Voronoi diagram calculation (in the form of precipitate free bisectors) is achieved, so there is no requirement for further processing to extract the calculation results. Previously it was assumed that the permanence of the results was also a potenti...
Semiconductor Quantum Dots in Chemical Sensors and Biosensors
Nikos Chaniotakis; Frasco, Manuela F.
2009-01-01
Quantum dots are nanometre-scale semiconductor crystals with unique optical properties that are advantageous for the development of novel chemical sensors and biosensors. The surface chemistry of luminescent quantum dots has encouraged the development of multiple probes based on linked recognition molecules such as peptides, nucleic acids or small-molecule ligands. This review overviews the design of sensitive and selective nanoprobes, ranging from the type of target molecules to the optical ...
Semiconductor Quantum Dots in Chemical Sensors and Biosensors
Directory of Open Access Journals (Sweden)
Nikos Chaniotakis
2009-09-01
Full Text Available Quantum dots are nanometre-scale semiconductor crystals with unique optical properties that are advantageous for the development of novel chemical sensors and biosensors. The surface chemistry of luminescent quantum dots has encouraged the development of multiple probes based on linked recognition molecules such as peptides, nucleic acids or small-molecule ligands. This review overviews the design of sensitive and selective nanoprobes, ranging from the type of target molecules to the optical transduction scheme. Representative examples of quantum dot-based optical sensors from this fast-moving field have been selected and are discussed towards the most promising directions for future research.
Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines
DEFF Research Database (Denmark)
Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;
2011-01-01
Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation....... This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. 1Δ15N(D) and 2Δ1H(D) of the NH3+ groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show...
Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy
Piccini, GiovanniMaria; Alessio, Maristella
2016-01-01
Abstract The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude). PMID:27008460
Approaching Chemical Accuracy with Quantum Monte Carlo
Petruzielo, Frank R.; Toulouse, Julien; Umrigar, C. J.
2012-01-01
International audience; A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreem...
Chemical accuracy from quantum Monte Carlo for the Benzene Dimer
Azadi, Sam; Cohen, R. E
2015-01-01
We report an accurate study of interactions between Benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory (DFT) using different van der Waals (vdW) functionals. In our QMC calculations, we use accurate correlated trial wave functions including three-body Jastrow factors, and backflow transformations. We consider two benzene molecules in the parallel displaced (PD) geometry, and fin...
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…
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…
pK(a) prediction from "Quantum Chemical Topology" descriptors.
Harding, A P; Wedge, D C; Popelier, P L A
2009-08-01
Knowing the pK(a) of a compound gives insight into many properties relevant to many industries, in particular the pharmaceutical industry during drug development processes. In light of this, we have used the theory of Quantum Chemical Topology (QCT), to provide ab initio descriptors that are able to accurately predict pK(a) values for 228 carboxylic acids. This Quantum Topological Molecular Similarity (QTMS) study involved the comparison of 5 increasingly more expensive levels of theory to conclude that HF/6-31G(d) and B3LYP/6-311+G(2d,p) provided an accurate representation of the compounds studies. We created global and subset models for the carboxylic acids using Partial Least Square (PLS), Support Vector Machines (SVM), and Radial Basis Function Neural Networks (RBFNN). The models were extensively validated using 4-, 7-, and 10-fold cross-validation, with the validation sets selected based on systematic and random sampling. HF/6-31G(d) in conjunction with SVM provided the best statistics when taking into account the large increase in CPU time required to optimize the geometries at the B3LYP/6-311+G(2d,p) level. The SVM models provided an average q(2) value of 0.886 and an RMSE value of 0.293 for all the carboxylic acids, a q(2) of 0.825 and RMSE of 0.378 for the ortho-substituted acids, a q(2) of 0.923 and RMSE of 0.112 for the para- and meta-substituted acids, and a q(2) of 0.906 and RMSE of 0.268 for the aliphatic acids. Our method compares favorably to ACD/Laboratories, VCCLAB, SPARC, and ChemAxon's pK(a) prediction software based of the RMSE calculated by the leave-one-out method.
The quantum dynamics of electronically nonadiabatic chemical reactions
Truhlar, Donald G.
1993-01-01
Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally
GPU accelerated chemical similarity calculation for compound library comparison.
Ma, Chao; Wang, Lirong; Xie, Xiang-Qun
2011-07-25
Chemical similarity calculation plays an important role in compound library design, virtual screening, and "lead" optimization. In this manuscript, we present a novel GPU-accelerated algorithm for all-vs-all Tanimoto matrix calculation and nearest neighbor search. By taking advantage of multicore GPU architecture and CUDA parallel programming technology, the algorithm is up to 39 times superior to the existing commercial software that runs on CPUs. Because of the utilization of intrinsic GPU instructions, this approach is nearly 10 times faster than existing GPU-accelerated sparse vector algorithm, when Unity fingerprints are used for Tanimoto calculation. The GPU program that implements this new method takes about 20 min to complete the calculation of Tanimoto coefficients between 32 M PubChem compounds and 10K Active Probes compounds, i.e., 324G Tanimoto coefficients, on a 128-CUDA-core GPU.
DEFF Research Database (Denmark)
Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;
2013-01-01
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...
Calculation method of quantum efficiency to TiO2 nanocrystal photocatalysis reaction
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
The quantum yield is an important factor to evaluate the efficiency of photoreactor. This article gives an overall calculation method of the quantum efficiency(ф) and the apparent quantum efficiency(ф2) to the TiO2/UV photocatalysis system. Furthermore, for the immobility system (IS), the formulation of the faction of light absorbed by the TiO2 thin film is proposed so as to calculate the quantum efficiency by using the measured value and theoretic calculated value of transmissivity (T). For the suspension system(SS), due to the difficulty to obtain the absorption coefficient (α) of TiO2 particulates, the quantum efficiency is calculated by means of the relative photonic efficiency (ξr) and the standard quantum yield (фstandard).
Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations
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.
Quantum-Chemical Insights from Deep Tensor Neural Networks
Schütt, Kristof T; Chmiela, Stefan; Müller, Klaus R; Tkatchenko, Alexandre
2016-01-01
Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text, and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks (DTNN), which leads to size-extensive and uniformly accurate (1 kcal/mol) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the DTNN model reveals a classification of aromatic rings with respect to their stability -- a useful property that is not contained as such in the training dataset. Further applications of DTNN for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies...
Superiority of semiclassical over quantum mechanical calculations for a three-dimensional system
Energy Technology Data Exchange (ETDEWEB)
Main, Joerg; Wunner, Guenter; Atilgan, Erdinc; Taylor, Howard S.; Dando, Paul A
2002-12-02
In systems with few degrees of freedom modern quantum calculations are, in general, numerically more efficient than semiclassical methods. However, this situation can be reversed with increasing dimension of the problem. For a three-dimensional system, viz. the hyperbolic four-sphere scattering system, we demonstrate the superiority of semiclassical versus quantum calculations. Semiclassical resonances can easily be obtained even in energy regions which are unattainable with the currently available quantum techniques.
Superiority of semiclassical over quantum mechanical calculations for a three-dimensional system
Main, Jörg; Wunner, Günter; Atılgan, Erdinç; Taylor, Howard S.; Dando, Paul A.
2002-12-01
In systems with few degrees of freedom modern quantum calculations are, in general, numerically more efficient than semiclassical methods. However, this situation can be reversed with increasing dimension of the problem. For a three-dimensional system, viz. the hyperbolic four-sphere scattering system, we demonstrate the superiority of semiclassical versus quantum calculations. Semiclassical resonances can easily be obtained even in energy regions which are unattainable with the currently available quantum techniques.
Chemical application of diffusion quantum Monte Carlo
Reynolds, P. J.; Lester, W. A., Jr.
1983-10-01
The diffusion quantum Monte Carlo (QMC) method gives a stochastic solution to the Schroedinger equation. As an example the singlet-triplet splitting of the energy of the methylene molecule CH2 is given. The QMC algorithm was implemented on the CYBER 205, first as a direct transcription of the algorithm running on our VAX 11/780, and second by explicitly writing vector code for all loops longer than a crossover length C. The speed of the codes relative to one another as a function of C, and relative to the VAX is discussed. Since CH2 has only eight electrons, most of the loops in this application are fairly short. The longest inner loops run over the set of atomic basis functions. The CPU time dependence obtained versus the number of basis functions is discussed and compared with that obtained from traditional quantum chemistry codes and that obtained from traditional computer architectures. Finally, preliminary work on restructuring the algorithm to compute the separate Monte Carlo realizations in parallel is discussed.
The genesis of the quantum theory of the chemical bond
Esposito, S
2013-01-01
An historical overview is given of the relevant steps that allowed the genesis of the quantum theory of the chemical bond, starting from the appearance of the new quantum mechanics and following later developments till approximately 1931. General ideas and some important details are discussed concerning molecular spectroscopy, as well as quantum computations for simple molecular systems performed within perturbative and variational approaches, for which the Born-Oppenheimer method provided a quantitative theory accounting for rotational, vibrational and electronic states. The novel concepts introduced by the Heitler-London theory, complemented by those underlying the method of the molecular orbitals, are critically analyzed along with some of their relevant applications. Further improvements in the understanding of the nature of the chemical bond are also considered, including the ideas of one-electron and three-electron bonds introduced by Pauling, as well as the generalizations of the Heitler-London theory ...
Quantum chemical approach to estimating the thermodynamics of metabolic reactions.
Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán
2014-11-12
Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.
Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions
Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán
2014-01-01
Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism. PMID:25387603
Periodic quantum chemical studies on anhydrous and hydrated acid clinoptilolite.
Valdiviés Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M
2014-08-07
Periodic quantum chemistry methods as implemented in the crystal09 code were considered to study acid clinoptilolite (HEU framework type), both anhydrous and hydrated. The most probable location of acid sites and water molecules together with other structural details has been the object of particular attention. Calculations were performed at hybrid and pristine DFT levels of theory with a VDZP quality basis set in order to compare performances. It arises that PBE0 provides the best agreement with experimental data as concerns structural features and the most stable Al distribution in the framework. The role of the water molecule distribution in the stability of the systems, the most probable structure that they induce in the material, and their eventual influence on further chemical modification processes, such as dealumination, are discussed in detail. Results show that, apart from the usually considered interactions of water molecules with the zeolite framework, that is, a H-bond with Brönsted acid sites and coordination with framework Al as Lewis ones, it is necessary to consider cooperation of other weaker effects so as to fully understand the hydration effect in this kind of materials.
Quantum chemical studies of photochromic properties of benzoxazine compound
Energy Technology Data Exchange (ETDEWEB)
Toliautas, Stepas, E-mail: stepas.toliautas@ff.stud.vu.lt [Department of Theoretical Physics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania); Sulskus, Juozas, E-mail: juozas.sulskus@ff.vu.lt [Department of Theoretical Physics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania); Valkunas, Leonas, E-mail: leonas.valkunas@ff.vu.lt [Department of Theoretical Physics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania); Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300 Vilnius (Lithuania); Vengris, Mikas, E-mail: mikas.vengris@ff.vu.lt [Department of Quantum Electronics, Vilnius University, Sauletekio 9-III, LT-10222 Vilnius (Lithuania)
2012-08-24
Highlights: Black-Right-Pointing-Pointer Photochromic indolo-benzoxazine compound is studied. Black-Right-Pointing-Pointer Advanced LC-TDDFT and GMC-QDPT methods are used for excited state calculations. Black-Right-Pointing-Pointer Oxazine ring opens upon UV light excitation. Black-Right-Pointing-Pointer Fragments of the compound assume structures similar to the ions of separate molecules. Black-Right-Pointing-Pointer Multiple pathways of the photo-induced reaction are expected. -- Abstract: Molecular electronic structure of ground and excited states of a photochromic indolo[2,1-b][1,3]benzoxazine compound incorporating closed-ring system, which opens upon UV light excitation, was studied using various quantum chemical methods. Three local minima of the ground electronic state potential energy surface and related transition states were identified along the path of rotation of 4-nitrophenol group. Additionally, three local minima of the excited electronic states were located. The evaluated transition energy barriers between local ground-state minima nearest to the initial structure of the investigated molecule are less than 2 k{sub B}T, making open structures likely to revert to the initial structure by thermalization. Results obtained using ab initio GMC-QDPT method were explored and compared to the widely used TD-DFT and semi-empiric ZINDO methods.
Quantum chemical studies on the reactivity of oxazole derivatives
Hosseinzadeh, Behzad; Eskandari, Khalil; Zarandi, Maryam; Asli, Reza
2016-11-01
The quantum chemical study of the reactivity of a series of oxazole derivatives substituted at 2, 4, and 5 positions was performed using B3LYP/6-311++G( d, p) and MP2/6-311++G( d, p) levels of theory. Different substituents have been applied to cover a wide range of electronic effects. On the basis of Fukui functions, oxazole derivatives in the gas phase are found to be suitable nucleophilic sites. For the most of studied substituents, it was observed that the calculated Fukui function f k - values at the N-position are small in case of electron-withdrawing substituents, resulting a preferred N-position for hard reactions. In contrast, large f k - values in case of electron-donating groups show a preferred N-position for soft reactions. These two local reactivity descriptors predicted the reactivity of the electron-rich oxazoles sequence to be 2-substituted oxazoles > 5-substituted oxazoles > 4-substituted oxazoles, where due to resonance effect, the reactivity toward electrophilic attack at the pyridine nitrogen atom is enhanced by electron donor substituents.
Dynamical mean-field theory from a quantum chemical perspective.
Zgid, Dominika; Chan, Garnet Kin-Lic
2011-03-07
We investigate the dynamical mean-field theory (DMFT) from a quantum chemical perspective. Dynamical mean-field theory offers a formalism to extend quantum chemical methods for finite systems to infinite periodic problems within a local correlation approximation. In addition, quantum chemical techniques can be used to construct new ab initio Hamiltonians and impurity solvers for DMFT. Here, we explore some ways in which these things may be achieved. First, we present an informal overview of dynamical mean-field theory to connect to quantum chemical language. Next, we describe an implementation of dynamical mean-field theory where we start from an ab initio Hartree-Fock Hamiltonian that avoids double counting issues present in many applications of DMFT. We then explore the use of the configuration interaction hierarchy in DMFT as an approximate solver for the impurity problem. We also investigate some numerical issues of convergence within DMFT. Our studies are carried out in the context of the cubic hydrogen model, a simple but challenging test for correlation methods. Finally, we finish with some conclusions for future directions.
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.
Li, Shenggang; Zhai, Hua-Jin; Wang, Lai-Sheng; Dixon, David A
2009-10-22
We report a comparative study of reduced transition metal oxide clusters, M(3)O(8)(-) (M = Cr, W) anions and their neutrals, via anion photoelectron spectroscopy (PES) and density functional theory (DFT) and molecular orbital theory (CCSD(T)) calculations. Well-resolved PES spectra are obtained for M(3)O(8)(-) (M = Cr, W) at 193 and 157 nm photon energies. Different PES spectra are observed for M = Cr versus M = W. Extensive DFT and CCSD(T) calculations are performed to locate the ground and low-lying excited states for the neutrals and anions. The ground states of Cr(3)O(8) and Cr(3)O(8)(-) are predicted to be the (3)B(2) and (4)B(2) states of a C(2v) structure, respectively, revealing ferromagnetic spin coupling for Cr 3d electrons. In contrast, the ground states of W(3)O(8) and W(3)O(8)(-) are predicted to be the (1)A' state (C(s) symmetry) and the (2)A(1) state (C(2v) symmetry), respectively, showing metal-metal d-d bonding in the anion. The current cluster geometries are in qualitative agreement with prior DFT studies at the PBE level for M = Cr and the B3LYP level for M = W. The BP86 and PW91 functionals significantly outperform the B3LYP functional for the Cr species, in terms of relative energies, electron detachment energies, and electronic excitation energies, whereas the B3LYP functional is better for the W species. Accurate heats of formation for the ground states of M(3)O(8) are calculated from the clustering energies and the heats of formation of MO(2) and MO(3). The energetics have been used to predict redox reaction thermochemistry.
Dorofeeva, O. V.; Ryzhova, O. N.; Moiseeva, N. F.
2008-06-01
The enthalpies of formation, entropies, and heat capacities of 95 organophosphorus derivatives calculated by nonempirical quantum-chemical methods were used to develop the additive method for estimating the thermodynamic properties of these compounds. 86 group contribution values were obtained for estimating the thermodynamic properties of diverse organic derivatives of phosphorus in the oxidation states 3 and 5 (three-and four-coordinate phosphorus atoms).
Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.
Knizia, Gerald
2013-11-12
Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (χ), C 1s core-level shifts, resonance substituent parameters (σR), Lewis structures, and oxidation states of transition-metal complexes.
Quantum-chemical insights from deep tensor neural networks
Schütt, Kristof T.; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R.; Tkatchenko, Alexandre
2017-01-01
Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol−1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems. PMID:28067221
Asymmetric chemical reactions by polarized quantum beams
Takahashi, Jun-Ichi; Kobayashi, Kensei
One of the most attractive hypothesis for the origin of homochirality in terrestrial bio-organic compounds (L-amino acid and D-sugar dominant) is nominated as "Cosmic Scenario"; a chiral impulse from asymmetric excitation sources in space triggered asymmetric reactions on the surfaces of such space materials as meteorites or interstellar dusts prior to the existence of terrestrial life. 1) Effective asymmetric excitation sources in space are proposed as polarized quantum beams, such as circularly polarized light and spin polarized electrons. Circularly polarized light is emitted as synchrotron radiation from tightly captured electrons by intense magnetic field around neutron stars. In this case, either left-or right-handed polarized light can be observed depending on the direction of observation. On the other hand, spin polarized electrons is emitted as beta-ray in beta decay from radioactive nuclei or neutron fireballs in supernova explosion. 2) The spin of beta-ray electrons is longitudinally polarized due to parity non-conservation in the weak interaction. The helicity (the the projection of the spin onto the direction of kinetic momentum) of beta-ray electrons is universally negative (left-handed). For the purpose of verifying the asymmetric structure emergence in bio-organic compounds by polarized quantum beams, we are now carrying out laboratory simulations using circularly polarized light from synchrotron radiation facility or spin polarized electron beam from beta-ray radiation source. 3,4) The target samples are solid film or aqueous solution of racemic amino acids. 1) K.Kobayashi, K.Kaneko, J.Takahashi, Y.Takano, in Astrobiology: from simple molecules to primitive life; Ed. V.Basiuk; American Scientific Publisher: Valencia, 2008. 2) G.A.Gusev, T.Saito, V.A.Tsarev, A.V.Uryson, Origins Life Evol. Biosphere. 37, 259 (2007). 3) J.Takahashi, H.Shinojima, M.Seyama, Y.Ueno, T.Kaneko, K.Kobayashi, H.Mita, M.Adachi, M.Hosaka, M.Katoh, Int. J. Mol. Sci. 10, 3044
Accounting for chemical kinetics in field scale transport calculations
Energy Technology Data Exchange (ETDEWEB)
Bryan, N.D. [Manchester Univ. (United Kingdom). Dept. of Chemistry
2005-04-01
The modelling of column experiments has shown that the humic acid mediated transport of metal ions is dominated by the non-exchangeable fraction. Metal ions enter this fraction via the exchangeable fraction, and may transfer back again. However, in both directions these chemical reactions are slow. Whether or not a kinetic description of these processes is required during transport calculations, or an assumption of local equilibrium will suffice, will depend upon the ratio of the reaction half-time to the residence time of species within the groundwater column. If the flow rate is sufficiently slow or the reaction sufficiently fast then the assumption of local equilibrium is acceptable. Alternatively, if the reaction is sufficiently slow (or the flow rate fast), then the reaction may be 'decoupled', i.e. removed from the calculation. These distinctions are important, because calculations involving chemical kinetics are computationally very expensive, and should be avoided wherever possible. In addition, column experiments have shown that the sorption of humic substances and metal-humate complexes may be significant, and that these reactions may also be slow. In this work, a set of rules is presented that dictate when the local equilibrium and decoupled assumptions may be used. In addition, it is shown that in all cases to a first approximation, the behaviour of a kinetically controlled species, and in particular its final distribution against distance at the end of a calculation, depends only upon the ratio of the reaction first order rate to the residence time, and hence, even in the region where the simplifications may not be used, the behaviour is predictable. In this way, it is possible to obtain an estimate of the migration of these species, without the need for a complex transport calculation. (orig.)
Quantum control and entanglement in a chemical compass
Cai, Jianming; Briegel, Hans J
2009-01-01
The radical pair mechanism is one of the two main hypotheses to explain the navigability of animals in weak magnetic fields, enabling e.g. birds to see the Earth's magnetic field. We show how quantum control can be used to either enhance or reduce the performance of such a chemical compass, providing a route to further test this hypothesis experimentally. We investigate the dynamics of quantum entanglement in this model, and demonstrate intriguing connections between radical-pair entanglement and the magnetic field sensitivity of the compass. The nature of the nuclear-spin environment plays an essential role for the observed effects.
Indian Academy of Sciences (India)
DEVENDRA P MISHRA; ANCHAL SRIVASTAVA; R K SHUKLA
2017-07-01
This paper describes the spectroscopic ($_{1}\\rm{H}$ and $_{13}\\rm{C NMR}$, FT-IR and UV–Visible), chemical, nonlinear optical and thermodynamic properties of D-Myo-Inositol using quantum chemical technique and its experimental verification. The structural parameters of the compound are determined from the optimized geometry by B3LYP method with $6-311++G(d,p)$ basis set. It was found that the optimized parameters thus obtained are almost in agreement with the experimental ones. A detailed interpretation of the infrared spectra of D-Myo-Inositol is also reported in the present work. After optimization, the proton and carbon NMR chemical shifts of the studied compound are calculated using GIAO and 6-311++G(d,p) basis set. The search of organic materials with improved charge transfer properties requires precise quantum chemical calculations of space-charge density distribution, state and transition dipole moments and HOMO–LUMO states. The nature of the transitions in the observed UV–Visible spectrum of the compound has been studied by the time-dependent density functional theory (TD-DFT). The global reactivity descriptors like chemical potential, electronegativity, hardness, softness and electrophilicity index, have been calculated using DFT. The thermodynamic calculation related to the title compound was also performed at $B3LYP/6-311++G(d,p)$ level of theory. The standard statistical thermodynamic functions like heat capacity at constant pressure, entropy and enthalpy change were obtained from the theoretical harmonic frequencies of the optimized molecule. It is observed that the values of heat capacity, entropy and enthalpy increase with increase intemperature from 100 to 1000 K, which is attributed to the enhancement of molecular vibration with the increase in temperature.
Mishra, Devendra P.; Srivastava, Anchal; Shukla, R. K.
2017-07-01
This paper describes the spectroscopic (^1H and ^{13}C NMR, FT-IR and UV-Visible), chemical, nonlinear optical and thermodynamic properties of D-Myo-Inositol using quantum chemical technique and its experimental verification. The structural parameters of the compound are determined from the optimized geometry by B3LYP method with 6 {-}311{+}{+}G(d,p) basis set. It was found that the optimized parameters thus obtained are almost in agreement with the experimental ones. A detailed interpretation of the infrared spectra of D-Myo-Inositol is also reported in the present work. After optimization, the proton and carbon NMR chemical shifts of the studied compound are calculated using GIAO and 6 {-}311{+}{+}G(d,p) basis set. The search of organic materials with improved charge transfer properties requires precise quantum chemical calculations of space-charge density distribution, state and transition dipole moments and HOMO-LUMO states. The nature of the transitions in the observed UV-Visible spectrum of the compound has been studied by the time-dependent density functional theory (TD-DFT). The global reactivity descriptors like chemical potential, electronegativity, hardness, softness and electrophilicity index, have been calculated using DFT. The thermodynamic calculation related to the title compound was also performed at B3LYP/ 6 {-}311{+}{+}G(d,p) level of theory. The standard statistical thermodynamic functions like heat capacity at constant pressure, entropy and enthalpy change were obtained from the theoretical harmonic frequencies of the optimized molecule. It is observed that the values of heat capacity, entropy and enthalpy increase with increase in temperature from 100 to 1000 K, which is attributed to the enhancement of molecular vibration with the increase in temperature.
PDB ligand conformational energies calculated quantum-mechanically.
Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V; Liao, Chenzhong; Peach, Megan L; Ihlenfeldt, Wolf-Dietrich; Karki, Rajeshri G; Borodina, Yulia V; Cachau, Raul E; Nicklaus, Marc C
2012-03-26
(RSCC). We repeated these calculations with the solvent model IEFPCM, which yielded energy differences that were generally somewhat lower than the corresponding vacuum results but did not produce a qualitatively different picture. Torsional sampling around the crystal conformation at the molecular mechanics level using the MMFF94s force field typically led to an increase in energy. © 2012 American Chemical Society
Quantum Monte Carlo calculations of the dimerization energy of borane.
Fracchia, Francesco; Bressanini, Dario; Morosi, Gabriele
2011-09-07
Accurate thermodynamic data are required to improve the performance of chemical hydrides that are potential hydrogen storage materials. Boron compounds are among the most interesting candidates. However, different experimental measurements of the borane dimerization energy resulted in a rather wide range (-34.3 to -39.1) ± 2 kcal/mol. Diffusion Monte Carlo (DMC) simulations usually recover more than 95% of the correlation energy, so energy differences rely less on error cancellation than other methods. DMC energies of BH(3), B(2)H(6), BH(3)CO, CO, and BH(2)(+) allowed us to predict the borane dimerization energy, both via the direct process and indirect processes such as the dissociation of BH(3)CO. Our D(e) = -43.12(8) kcal/mol, corrected for the zero point energy evaluated by considering the anharmonic contributions, results in a borane dimerization energy of -36.59(8) kcal/mol. The process via the dissociation of BH(3)CO gives -34.5(2) kcal/mol. Overall, our values suggest a slightly less D(e) than the most recent W4 estimate D(e) = -44.47 kcal/mol [A. Karton and J. M. L. Martin, J. Phys. Chem. A 111, 5936 (2007)]. Our results show that reliable thermochemical data for boranes can be predicted by fixed node (FN)-DMC calculations.
Chemical bonding in TiSb(2) and VSb(2): a quantum chemical and experimental study.
Armbrüster, Marc; Schnelle, Walter; Schwarz, Ulrich; Grin, Yuri
2007-08-06
The chemical bonding in the isostructural intermetallic compounds TiSb2 and VSb2, crystallizing in the CuAl2 type, was investigated by means of quantum chemical calculations, particularly the electron localization function (ELF), as well as by Raman spectroscopy, Hall effect and conductivity measurements on oriented single crystals, and high-pressure X-ray powder diffraction. The homogeneity ranges of the compounds were determined by powder X-ray diffraction, WDXS, and DSC measurements. TiSb2 exhibits no significant homogeneity range, while VSb2 shows a small homogeneity range of approximately 0.3 at. %. According to the ELF calculations, the Sb atoms form dumbbells via a two-center two-electron bond, while the T atoms (T = Ti, V) build up chains along the crystallographic c-axis. Both building units are connected by covalent T-Sb-T three-center bonds, thus forming a three-dimensional network. The strength of the bonds involving Sb was determined by fitting a force constant model to the vibrational mode frequencies observed by polarized Raman measurements on oriented single crystals. The resulting bond order of the Sb2 dumbbells is 1, while the strength of the three-center bonds resembles a bond order of 1.5. The weak pressure dependence of the c/a ratio confirms the slightly different bonding picture in TiSb2 compared to that in CuAl2. Electrical transport measurements show the presence of free charge carriers, as well as a metal-like temperature dependence of the electrical resistivity.
Majorana, Pauling and the quantum theory of the chemical bond
Esposito, S
2013-01-01
We discuss in detail very little known results obtained by Majorana as early as 1931, regarding the quantum theory of the chemical bond in homopolar molecules, based on the key concept of exchange interaction. After a brief historical overview of the quantum homopolar valence theory, we address the intriguing issues of the formation of the helium molecular ion, He2+, and of the accurate description of the hydrogen molecule, H2. For the first case, the group theory-inspired approach used by Majorana is contrasted with that more known followed by Pauling (and published few months after that of Majorana), while for the second case we focus on his proposal concerning the possible existence of ionic structures in homopolar compounds, just as in the hydrogen molecule. The novelty and relevance of Majorana's results in the modern research on molecular and chemical physics is emphasized as well.
Delgado, Eduardo J; Alderete, Joel B
2003-01-01
The Henry's law constants (H) for triazine derived herbicides are calculated using quantum chemical solvation models, SM2, SM3, PCM-DFT, and CPCM-DFT, and their performances are discussed. The results show considerable differences in performance among the different levels of theory. The values of H calculated by the semiempirical methods agree much better with the experimental values than those obtained at the DFT level. The differences are discussed in terms of the different contributions, electrostatic and no-electrostatic, to Gibbs free energy of solvation. In addition, the Henry's law constants of some triazine derived herbicides whose values have not been reported earlier are predicted as well.
A perspective on quantum mechanics calculations in ADMET predictions.
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.
Calculating Two-Dimensional Spectra with the Mixed Quantum-Classical Ehrenfest Method
van der Vegte, C. P.; Dijkstra, A. G.; Knoester, J.; Jansen, T. L. C.
2013-01-01
We present a mixed quantum-classical simulation approach to calculate two-dimensional spectra of coupled two-level electronic model systems. We include the change in potential energy of the classical system due to transitions in the quantum system using the Ehrenfest method. We study how this
Chernyavskiy, A. Yu.
2013-01-01
The simple and universal global optimization method based on simplified multipopulation genetic algorithm is presented. The method is applied to quantum information problems. It is compared to the genetic algorithm on standard test functions, and also tested on the calculation of quantum discord and minimal entanglement entropy, which is an entanglement measure for pure multipartite states.
Calculation of Quantum Probability in O(2,2) String Cosmology with a Dilaton Potential
Institute of Scientific and Technical Information of China (English)
YAN Jun
2006-01-01
The quantum properties of O(2,2) string cosmology with a dilaton potential are studied in this paper. The cosmological solutions are obtained on three-dimensional space-time. Moreover, the quantum probability of transition between two duality universe is calculated through a Wheeler-De Witt approach.
Calculating Two-Dimensional Spectra with the Mixed Quantum-Classical Ehrenfest Method
van der Vegte, C. P.; Dijkstra, A. G.; Knoester, J.; Jansen, T. L. C.
2013-01-01
We present a mixed quantum-classical simulation approach to calculate two-dimensional spectra of coupled two-level electronic model systems. We include the change in potential energy of the classical system due to transitions in the quantum system using the Ehrenfest method. We study how this feedba
Murugavel, S.; Sundramoorthy, S.; Lakshmanan, D.; Subashini, R.; Pavan Kumar, P.
2017-03-01
The novel title compound 4-chloro-8-methoxyquinoline-2(1H)-one (4CMOQ) has been synthesized by slow evaporation solution growth technique at room temperature. The synthesized 4CMOQ molecule was characterized experimentally by FT-IR, FT-Raman, UV-Vis, NMR and single crystal diffraction (XRD) and theoretically by quantum chemical calculations. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311++G (d,p) basis set in ground state and compared with the experimental data. The entire vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED) by VEDA 4 programme. The nuclear magnetic resonance spectra (1H and 13C NMR) are obtained by using the gauge-invariant atomic orbital (GIAO) method. The change in electron density (ED) in the antibonding orbital's and stabilization energies E(2) of the molecule have been evaluated by natural bond orbital (NBO) analysis to give clear evidence of stabilization. Moreover, electronic characteristics such as HOMO and LUMO energies, Mulliken atomic charges and molecular electrostatic potential surface are investigated. Absorption spectrum analysis, nonlinear optical properties, chemical reactivity descriptors and thermodynamic features are also outlined theoretically. Molecular docking studies were executed to understand the inhibitory activity of 4CMOQ against DNA gyrase and Lanosterol 14 α-demethylase. The antimicrobial activity of 4CMOQ was determined against bacterial strains such as Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa and fungal strains such as Aspergillus niger, Monascus purpureus and Penicillium citrinum. The obtained results show that the compound exhibited good to moderate antimicrobial activity.
Morgado, Claudio A; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jirí
2010-04-14
We have performed reference quantum-chemical calculations for about 130 structures of adenine dimers in stacked conformations, with special attention given to dimers that are either vertically compressed (parallel structures) or contain close interatomic contacts (non-parallel structures). Such geometries are sampled during thermal fluctuations of nucleic acids and contribute to the local conformational variability of these systems. Their theoretical characterization requires a good description of interaction energies in the short-range repulsion region. The reference calculations have been performed with the CBS(T) method, i.e., MP2/CBS computations corrected for higher-order electron-correlation effects using the CCSD(T) method. These benchmark data have been used to examine the performance of the DFT-D, SCS(MI)-MP2, MP2.5, M06-2X and CBS(SCS-D) quantum-mechanical methods, and of the AMBER Cornell et al. force field. The present results, as well as those of our previous study on stacked uracil dimers, confirm that the force field severely exaggerates the repulsion at short intermolecular distances. This behavior complicates the use of the force field in scans of the stacking-energy dependence on local conformational parameters in nucleic acids. Compared against the previous results obtained in the uracil dimer study, the performance of DFT-D to describe stacking at short intermolecular distances has worsened, showing for the adenine dimers a larger exaggeration of the repulsion, especially for structures where the monomers are parallel to each other. Despite these deviations, the performance of DFT-D is still reasonably good and this method provides, for example, a relatively inexpensive way to monitor stacking energies along molecular dynamics trajectories. The best performers are the MP2.5, SCS(MI)-MP2, and CBS(SCS-D) methods. In addition, the energy profiles given by the SCS(MI)-MP2 and CBS(SCS-D) methods are the ones that most closely resemble the CBS(T) data
Indian Academy of Sciences (India)
P Malekmohammadi Nouri; M M Attar
2015-04-01
The corrosion inhibition effect of fluconazole (FLU) was investigated on steel in 1 M hydrochloric acid solution. Weight loss measurements and atomic force microscope analysis were utilized to investigate the corrosion inhibition properties and film formation behaviour of FLU. Quantum chemical approach was also used to calculate some electronic properties of the molecule in neutral and protonated form in order to find any correlation between the inhibition effect and molecular structure of FLU molecule. The results showed that FLU can act as a good corrosion inhibitor for steel in hydrochloric acid solution at different temperatures and it can inhibit steel corrosion up to 95%. The adsorption followed the Langmuir isotherm and the thermodynamic parameters were also determined and discussed. Quantum chemical studies showed that in adsorption process of FLU molecules, nitrogen and oxygen atoms and benzene ring act as active centres.
Directory of Open Access Journals (Sweden)
Vinod P. Raphael
2016-01-01
Full Text Available A heterocyclic phenylhydrazone 2-[(E-(2-phenylhydrazinylidenemethyl]pyridine (P2APH and its reduced form 2-[(2-phenylhydrazinylmethyl]pyridine (RP2APH were synthesized, characterized, and subjected to corrosion inhibition investigation on carbon steel (CS in 1 M HCl using gravimetric, polarization, electrochemical noise, quantum chemical, and surface studies. P2APH showed more inhibition capacity than RP2PPH. But RP2PPH was very stable in acid medium and showed pronounced corrosion inhibition efficacy for days. Energy of HOMO and LUMO, their difference, number of electrons transferred, electronegativity, chemical hardness, and so forth were evaluated by quantum chemical studies. Agreeable correlation was observed between the results of quantum chemical calculations and other corrosion monitoring techniques.
Pendás, A Martín; Francisco, E; Blanco, M A
2007-01-01
We analyze the response of a quantum group within a molecule to charge transfer by using the interacting quantum atoms approach (IQA), an energy partitioning scheme within the quantum theory of atoms in molecules (QTAM). It is shown that this response lies at the core of the concept of the functional group. The manipulation of fractional electron populations is carried out by using distribution functions for the electron number within the quantum basins. Several test systems are studied to show that similar chemical potential groups are characterized by similar energetic behavior upon interaction with other groups. The origin of the empirical additivity rules for group energies in simple hydrocarbons is also investigated. It turns out to rest on the independent saturation of both the self-energies and the interaction energies of the groups as the size of the chain increases. We also show that our results are compatible with the standard group energies of the QTAM.
The Calculation of Matrix Elements in Relativistic Quantum Mechanics
Ilarraza-Lomelí, A. C.; Valdés-Martínez, M. N.; Salas-Brito, A. L.; Martínez-y-Romero, R. P.; Núñez-Yépez, H. N
2001-01-01
Employing a relativistic version of a hypervirial result, recurrence relations for arbitrary non-diagonal radial hydrogenic matrix elements have recently been obtained in Dirac relativistic quantum mechanics. In this contribution honoring Professor L\\"owdin, we report on a new relation we have recently discovered between the matrix elements $$ and $$---where $\\beta$ is a Dirac matrix and the numbers distiguish between different radial eigenstates--- that allow for a simplification and hence f...
A Calculation of Cosmological Scale from Quantum Coherence
Energy Technology Data Exchange (ETDEWEB)
Lindesay, J
2004-07-23
We use general arguments to examine the energy scales for which a quantum coherent description of gravitating quantum energy units is necessary. The cosmological dark energy density is expected to decouple from the Friedman-Lemaitre energy density when the Friedman-Robertson-Walker scale expansion becomes sub-luminal at R = c, at which time the usual microscopic interactions of relativistic quantum mechanics (QED, QCD, etc) open new degrees of freedom. We assume that these microscopic interactions cannot signal with superluminal exchanges, only superluminal quantum correlations. The expected gravitational vacuum energy density at that scale would be expected to freeze out due to the loss of gravitational coherence. We define the vacuum energy which generates this cosmological constant to be that of a zero temperature Bose condensate at this gravitational de-coherence scale. We presume a universality throughout the universe in the available degrees of freedom determined by fundamental constants during its evolution. Examining the reverse evolution of the universe from the present, long before reaching Planck scale dynamics one expects major modifications from the de-coherent thermal equations of state, suggesting that the pre-coherent phase has global coherence properties. Since the arguments presented involve primarily counting of degrees of freedom, we expect the statistical equilibrium states of causally disconnected regions of space to be independently identical. Thus, there is no horizon problem associated with the lack of causal influences between spatially separated regions in this approach. The scale of the amplitude of fluctuations produced during de-coherence of cosmological vacuum energy are found to evolve to values consistent with those observed in cosmic microwave background radiation and galactic clustering.
Quantum theory of chemical reactions in the presence of electromagnetic fields
Tscherbul, T V
2008-01-01
We present a theory for rigorous quantum scattering calculations of probabilities for chemical reactions of atoms with diatomic molecules in the presence of an external electric field. The approach is based on the fully uncoupled basis set representation of the total wave function in the space-fixed coordinate frame, the Fock-Delves hyperspherical coordinates and adiabatic partitioning of the total Hamiltonian of the reactive system. The adiabatic channel wave functions are expanded in basis sets of hyperangular functions corresponding to different reaction arrangements and the interactions with external fields are included in each chemical arrangement separately. We apply the theory to examine the effects of electric fields on the chemical reactions of LiF molecules with H atoms and HF molecules with Li atoms at low temperatures and show that electric fields may enhance the probability of chemical reactions and modify reactive scattering resonances by coupling the rotational states of the reactants. Our prel...
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…
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…
Raub, Stephan; Steffen, Andreas; Kämper, Andreas; Marian, Christel M
2008-07-01
In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.
Devereux, Mike; Popelier, Paul L A; McLay, Iain M
2009-06-01
This paper introduces the 'Quantum Isostere Database' (QID), a Web-based tool designed to find bioisosteric fragment replacements for lead optimization using stored ab initio data. A wide range of original geometric, electronic, and calculated physical properties are stored for each fragment. Physical descriptors with clear meaning are chosen, such as distribution of electrostatic potential energy values across a fragment surface and geometric parameters to describe fragment conformation and shape from ab initio structures. Further fundamental physical properties are linked to broader chemical characteristics relevant to biological activity, such as H-bond donor and acceptor strengths. Additional properties with less easily interpretable links to biological activity are also stored to allow future development of QSAR/QSPR models for quantities such as pK(a) and solubility. Conformational dependence of the ab initio descriptors is explicitly dealt with by storing properties for a variety of low-energy conformers of each fragment. Capping groups are used in ab initio calculations to represent different chemical environments, based on background research into transferability of electronic descriptors [J. Comput. Chem. 2009, 30, 1300-1318]. The resulting database has a Web interface that allows medicinal chemists to enter a query fragment, select important chemical features, and retrieve a list of suggested replacements with similar chemical characteristics. Examples of known bioisosteric replacements correctly identified by the QID tool are given.
Quantum Monte Carlo diagonalization method as a variational calculation
Energy Technology Data Exchange (ETDEWEB)
Mizusaki, Takahiro; Otsuka, Takaharu [Tokyo Univ. (Japan). Dept. of Physics; Honma, Michio
1997-05-01
A stochastic method for performing large-scale shell model calculations is presented, which utilizes the auxiliary field Monte Carlo technique and diagonalization method. This method overcomes the limitation of the conventional shell model diagonalization and can extremely widen the feasibility of shell model calculations with realistic interactions for spectroscopic study of nuclear structure. (author)
A quantum informational approach for dissecting chemical reactions
Duperrouzel, Corinne; Boguslawski, Katharina; Barcza, Gergerly; Legeza, Örs; Ayers, Paul W
2014-01-01
We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected which allows us to monitor the interplay of back-bonding and $\\pi$-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.
Eddy, Nnabuk O; Ibok, Udo J; Ebenso, Eno E; El Nemr, Ahmed; El Ashry, El Sayed H
2009-09-01
The inhibition efficiency of some antibiotics against mild steel corrosion was studied using weight loss and quantum chemical techniques. Values of inhibition efficiency obtained from weight loss measurements correlated strongly with theoretical values obtained through semi empirical calculations. High correlation coefficients were also obtained between inhibition efficiency of the antibiotics and some quantum chemical parameters, including frontier orbital (E (HOMO) and E (LUMO)), dipole moment, log P, TNC and LSER parameters (critical volume and dipolar-polarisability factor), which indicated that these parameters affect the inhibition efficiency of the compounds. It was also found that quantitative structure activity relation can be used to adequately predict the inhibition effectiveness of these compounds.
Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence.
de la Lande, Aurélien; Řezáč, Jan; Lévy, Bernard; Sanders, Barry C; Salahub, Dennis R
2011-03-23
Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.
Confidence and efficiency scaling in Variational Quantum Monte Carlo calculations
Delyon, François; Holzmann, Markus
2016-01-01
Based on the central limit theorem, we discuss the problem of evaluation of the statistical error of Monte Carlo calculations using a time discretized diffusion process. We present a robust and practical method to determine the effective variance of general observables and show how to verify the equilibrium hypothesis by the Kolmogorov-Smirnov test. We then derive scaling laws of the efficiency illustrated by Variational Monte Carlo calculations on the two dimensional electron gas.
Confidence and efficiency scaling in variational quantum Monte Carlo calculations
Delyon, F.; Bernu, B.; Holzmann, Markus
2017-02-01
Based on the central limit theorem, we discuss the problem of evaluation of the statistical error of Monte Carlo calculations using a time-discretized diffusion process. We present a robust and practical method to determine the effective variance of general observables and show how to verify the equilibrium hypothesis by the Kolmogorov-Smirnov test. We then derive scaling laws of the efficiency illustrated by variational Monte Carlo calculations on the two-dimensional electron gas.
Biswas, P K; Gogonea, V
2005-10-22
We describe a regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical (QM)-molecular-mechanical (MM) calculations. To remedy the nonphysical QM/MM Coulomb interaction at short distances arising from a point electrostatic potential (ESP) charge of the MM atom and also to accommodate the effect of polarized MM atom in the coupling Hamiltonian, we propose a partial-wave expansion of the ESP charge and describe the effect of a s-wave expansion, extended over the covalent radius r(c), of the MM atom. The resulting potential describes that, at short distances, large scale cancellation of Coulomb interaction arises intrinsically from the localized expansion of the MM point charge and the potential self-consistently reduces to 1r(c) at zero distance providing a renormalization to the Coulomb energy near interatomic separations. Employing this renormalized Hamiltonian, we developed an interface between the Car-Parrinello molecular-dynamics program and the classical molecular-dynamics simulation program Groningen machine for chemical simulations. With this hybrid code we performed QM/MM calculations on water dimer, imidazole carbon monoxide (CO) complex, and imidazole-heme-CO complex with CO interacting with another imidazole. The QM/MM results are in excellent agreement with experimental data for the geometry of these complexes and other computational data found in literature.
The Bondons: The Quantum Particles of the Chemical Bond
Directory of Open Access Journals (Sweden)
Mihai V. Putz
2010-10-01
Full Text Available By employing the combined Bohmian quantum formalism with the U(1 and SU(2 gauge transformations of the non-relativistic wave-function and the relativistic spinor, within the Schrödinger and Dirac quantum pictures of electron motions, the existence of the chemical field is revealed along the associate bondon particle characterized by its mass (mΒ, velocity (vΒ, charge (eΒ, and life-time (tΒ. This is quantized either in ground or excited states of the chemical bond in terms of reduced Planck constant ħ, the bond energy Ebond and length Xbond, respectively. The mass-velocity-charge-time quaternion properties of bondons’ particles were used in discussing various paradigmatic types of chemical bond towards assessing their covalent, multiple bonding, metallic and ionic features. The bondonic picture was completed by discussing the relativistic charge and life-time (the actual zitterbewegung problem, i.e., showing that the bondon equals the benchmark electronic charge through moving with almost light velocity. It carries negligible, although non-zero, mass in special bonding conditions and towards observable femtosecond life-time as the bonding length increases in the nanosystems and bonding energy decreases according with the bonding length-energy relationship Ebond[kcal/mol]*Xbond[A]=182019, providing this way the predictive framework in which the particle may be observed. Finally, its role in establishing the virtual states in Raman scattering was also established.
Institute of Scientific and Technical Information of China (English)
朱玉兰; 夏克; 周鑫鑫; 曹丽; 卢明祝; 王琨
2012-01-01
A new -(4,5-dibenzyldithio-l,3-dithiol-2-yIidene)naphthopyranone (3) has been synthesized. The moleculai structure was identified and characterized by UV-Vis, 1H NMR, 13C NMR, IR and TOFMS techniques. The electronic spectra, thermostability and fluorescence spectroscopy of 3 were briefly studied. The geometric structure of the product was optimized using Gaussian 03 quantum chemical program package with the method of density functional theory (DFT) at the B3PW91 level. The calculating results are in agreement with the experimental values. The research shows that 3 displays an intramolecular charge-transfer transition and remarkable fluorescence properies which were instructive explorations for pursuing new luminescent materials.%设计合成了一种新的具有D-π-A体系的有机分子:3-(4,5-二苄硫基-1,3-二硫杂环戊烯-2-亚基)萘吡喃酮,通过UV-vis,1H NMR,13C NMR TOFMS和IR确定了其结构.初步研究了该化合物的电子光谱、荧光光谱和热稳定性.运用Gaussian 03量子化学程序包,采用密度泛函(DFT) B3PW91的方法优化了其基态几何结构,得到的几何参数与实验结果吻合得很好.研究结果表明,体系中存在着分子内的电荷转移,有较好的荧光性质,为寻找新的发光材料具有一定的实际意义.
Efficient algorithms for large-scale quantum transport calculations
Brück, Sascha; Calderara, Mauro; Bani-Hashemian, Mohammad Hossein; VandeVondele, Joost; Luisier, Mathieu
2017-08-01
Massively parallel algorithms are presented in this paper to reduce the computational burden associated with quantum transport simulations from first-principles. The power of modern hybrid computer architectures is harvested in order to determine the open boundary conditions that connect the simulation domain with its environment and to solve the resulting Schrödinger equation. While the former operation takes the form of an eigenvalue problem that is solved by a contour integration technique on the available central processing units (CPUs), the latter can be cast into a linear system of equations that is simultaneously processed by SplitSolve, a two-step algorithm, on general-purpose graphics processing units (GPUs). A significant decrease of the computational time by up to two orders of magnitude is obtained as compared to standard solution methods.
Linear scaling calculation of an n-type GaAs quantum dot.
Nomura, Shintaro; Iitaka, Toshiaki
2007-09-01
A linear scale method for calculating electronic properties of large and complex systems is introduced within a local density approximation. The method is based on the Chebyshev polynomial expansion and the time-dependent method, which is tested on the calculation of the electronic structure of a model n-type GaAs quantum dot.
Calculation Model for Current-voltage Relation of Silicon Quantum-dots-based Nano-memory
Institute of Scientific and Technical Information of China (English)
YANG Hong-guan; DAI Da-kang; YU Biao; SHANG Lin-lin; GUO You-hong
2007-01-01
Based on the capacitive coupling formalism, an analytic model for calculating the drain currents of the quantum-dots floating-gate memory cell is proposed. Using this model, one can calculate numerically the drain currents of linear, saturation and subthreshold regions of the device with/without charges stored on the floating dots. The read operation process of an n-channel Si quantum-dots floating-gate nano-memory cell is discussed after calculating the drain currents versus the drain to source voltages and control gate voltages in both high and low threshold states respectively.
Fast and accurate calculation of dilute quantum gas using Uehling-Uhlenbeck model equation
Yano, Ryosuke
2017-02-01
The Uehling-Uhlenbeck (U-U) model equation is studied for the fast and accurate calculation of a dilute quantum gas. In particular, the direct simulation Monte Carlo (DSMC) method is used to solve the U-U model equation. DSMC analysis based on the U-U model equation is expected to enable the thermalization to be accurately obtained using a small number of sample particles and the dilute quantum gas dynamics to be calculated in a practical time. Finally, the applicability of DSMC analysis based on the U-U model equation to the fast and accurate calculation of a dilute quantum gas is confirmed by calculating the viscosity coefficient of a Bose gas on the basis of the Green-Kubo expression and the shock layer of a dilute Bose gas around a cylinder.
Concept of chemical bond and aromaticity based on quantum information theory
Szilvási, T; Legeza, Ö
2015-01-01
Quantum information theory (QIT) emerged in physics as standard technique to extract relevant information from quantum systems. It has already contributed to the development of novel fields like quantum computing, quantum cryptography, and quantum complexity. This arises the question what information is stored according to QIT in molecules which are inherently quantum systems as well. Rigorous analysis of the central quantities of QIT on systematic series of molecules offered the introduction of the concept of chemical bond and aromaticity directly from physical principles and notions. We identify covalent bond, donor-acceptor dative bond, multiple bond, charge-shift bond, and aromaticity indicating unified picture of fundamental chemical models from ab initio.
Quantum chemical studies of trace gas adsorption on ice nanoparticles
Schrems, Otto; Ignatov, Stanislav K.; Gadzhiev, Oleg B.; Masunov, Artem E.
2013-04-01
We have investigated the interaction of atmospheric trace gases with crystalline water ice particles of nanoscale size by modern quantum chemical methods. Small ice particles which can be formed in different altitudes play an important role in chemistry and physics of the Earth atmosphere. Knowledge about the uptake and incorporation of atmospheric trace gases in ice particles as well as their interactions with water molecules is very important for the understanding of processes at the air/ice interface. The interaction of the atmospheric trace gases with atmospheric ice nanoparticles is also an important issue for the development of modern physicochemical models. Usually, the interactions between trace gases and small particles considered theoretically apply small-size model complexes or the surface models representing only fragments of the ideal surface. Ice particles consisting of 48, 72, 216 and 270 water molecules with a distorted structure of hexagonal water ice Ih were studied using the new SCC-DFTBA method combining well the advantages of the DFT theory and semiempirical methods of quantum chemistry. The largest clusters correspond to the minimal nanoparticle size which are considered to be crystalline as determined experimentally. The clusters up to (H2O)72 were studied at the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(2d,2p) levels. The larger clusters were studied using DFTBA and DFTB+ methods. Several adsorption complexes for the (H2O)270 water ice cluster were optimized at the RI-BLYP/6-31+G(d) theory level to verify the DFTB+ results. Trace gas molecules were coordinated on different sites of the nanoparticles corresponding to different ice Ih crystal planes: (0001), (10-10), (11-20). As atmospheric trace gases we have chosen CO, CO2, HCO*, HCOH*, HCHO, HCOOH and (HCO)2. which are the possible products and intermediates of the UV photolysis of organic molecules such as HCHCHO adsorbed on the ice surface. The structures of the corresponding coordination
Quantum Monte Carlo calculations of two neutrons in finite volume
Klos, P; Tews, I; Gandolfi, S; Gezerlis, A; Hammer, H -W; Hoferichter, M; Schwenk, A
2016-01-01
Ab initio calculations provide direct access to the properties of pure neutron systems that are challenging to study experimentally. In addition to their importance for fundamental physics, their properties are required as input for effective field theories of the strong interaction. In this work, we perform auxiliary-field diffusion Monte Carlo calculations of the ground and first excited state of two neutrons in a finite box, considering a simple contact potential as well as chiral effective field theory interactions. We compare the results against exact diagonalizations and present a detailed analysis of the finite-volume effects, whose understanding is crucial for determining observables from the calculated energies. Using the L\\"uscher formula, we extract the low-energy S-wave scattering parameters from ground- and excited-state energies for different box sizes.
Energy Technology Data Exchange (ETDEWEB)
Nguyen, H.D.
1991-11-01
Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.
Energy Technology Data Exchange (ETDEWEB)
Nguyen, H.D.
1991-11-01
Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.
Grid-based methods for biochemical ab initio quantum chemical applications
Energy Technology Data Exchange (ETDEWEB)
Colvin, M.E.; Nelson, J.S.; Mori, E. [and others
1997-01-01
A initio quantum chemical methods are seeing increased application in a large variety of real-world problems including biomedical applications ranging from drug design to the understanding of environmental mutagens. The vast majority of these quantum chemical methods are {open_quotes}spectral{close_quotes}, that is they describe the charge distribution around the nuclear framework in terms of a fixed analytic basis set. Despite the additional complexity they bring, methods involving grid representations of the electron or solvent charge can provide more efficient schemes for evaluating spectral operators, inexpensive methods for calculating electron correlation, and methods for treating the electrostatic energy of salvation in polar solvents. The advantage of mixed or {open_quotes}pseudospectral{close_quotes} methods is that they allow individual non-linear operators in the partial differential equations, such as coulomb operators, to be calculated in the most appropriate regime. Moreover, these molecular grids can be used to integrate empirical functionals of the electron density. These so-called density functional methods (DFT) are an extremely promising alternative to conventional post-Hartree Fock quantum chemical methods. The introduction of a grid at the molecular solvent-accessible surface allows a very sophisticated treatment of a polarizable continuum solvent model (PCM). Where most PCM approaches use a truncated expansion of the solute`s electric multipole expansion, e.g. net charge (Born model) or dipole moment (Onsager model), such a grid-based boundary-element method (BEM) yields a nearly exact treatment of the solute`s electric field. This report describes the use of both DFT and BEM methods in several biomedical chemical applications.
Avramidi, I G
1994-01-01
We continue the development of the effective covariant methods for calculating the heat kernel and the one-loop effective action in quantum field theory and quantum gravity. The status of the low-energy approximation in quantum gauge theories and quantum gravity is discussed in detail on the basis of analyzing the local Schwinger - De Witt expansion. It is argued that the low-energy limit, when defined in a covariant way, should be related to background fields with covariantly constant curvature, gauge field strength and potential. Some new approaches for calculating the low-energy heat kernel assuming a covariantly constant background are proposed. The one-loop low-energy effective action in Yang-Mills theory in flat space with arbitrary compact simple gauge group and arbitrary matter on a covariantly constant background is calculated. The stability problem of the chromomagnetic (Savvidy-type) vacuum is analyzed. It is shown, that this type of vacuum structure can be stable only in the case when more than on...
Shugurov, S M; Panin, A I; Lopatin, S I; Emelyanova, K A
2015-06-07
The stabilities of gaseous germanium and tin vanadates were confirmed by high temperature mass spectrometry, and its structures were determined by quantum chemical calculations. A number of gas-phase reactions involving these gaseous salts were studied. On the basis of the equilibrium constants, the standard formation enthalpies of gaseous GeV2O6 (-1520 ± 42 kJ mol(-1)) and SnV2O6 (-1520 ± 43 kJ mol(-1)) were determined at a temperature of 298 K.
Quantum-chemistry calculations of hydrogen adsorption in MOF-5.
Gomez, Diego A; Combariza, Aldo F; Sastre, German
2009-10-28
High concentrations of molecular hydrogen adsorption on MOF-5 were evaluated at the semiempirical PM6 (periodic and cluster) and ab initio MP2 (cluster) theoretical levels. From the semiempirical calculations, an uptake of 3.9% weight on the inorganic building unit of MOF-5 was estimated, in good agreement with a recent accurate estimation of 4.5-5.2%. Although PM6 allows a correct estimation of the maximum uptake, the adsorption energy was overestimated and hence ab initio calculations, including a correlation treatment at the MP2 level as well as corrections for basis set superposition error, were performed with full optimisation, including the 6-31G basis set, which rendered an adsorption energy (per hydrogen molecule) of -0.14 kcal mol(-1). The crucial role of the quality of the basis set, as well as the importance of simulating high hydrogen loading (resembling experimental measurements), are remarked. Single point calculations (using the 6-31G geometry) with improved basis sets 6-31G(d,p) and 6-31++G(d,p) yielded adsorption energies of -0.33 and -0.57 kcal mol(-1), the latter in reasonable agreement with a recent experimental estimation of -1.0 kcal mol(-1). The role of the intermolecular hydrogen interactions is highlighted in this study, since many previous computational studies were performed at low hydrogen loadings, far from the experimental uptake conditions.
Quantum Chemistry Calculation of Angiotensin Converting Enzyme Inhibitors
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
@@Angiotensin Converting-Enzyme （ACE） inhibitors are potential drugs for hypertension.There are three requirements to be necessary for successful inhibition of ACE:1) a functional group capable of binding to zine in the active site (i.e.carboxylate,phosphonate,or sulfhydryl);2) a carbonyl oxygen capable of accepting a hydryogen bond from some donor residue functional groups and 3) an ionizable C-terminal carboxylate moiety which interacts with positively charged residue〔1〕. We reported active conformers of some ACE inhibitor molecules,which were derived by Distance Comparison〔2〕.In this paper,the electronic structure of the lowest energy conformers and active conformers of the ACE inhibitor molecules (Figure 1) were calculated through ab initio calculation by using Gaussian94 package.The Density Functional Theory (DFT) method and 6-31G** basis set were used 〔3〕.The calculation results were listed in Table 1.The total energies、HOMO energies and the charges of the marked atoms of all active conformers were higher than that of the correspondent lowest energy conformers.They were useful clues for designing novel analogs to inhibit the activity of ACE.
Quantum chemical study of a derivative of 3-substituted dithiocarbamic flavanone
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.
Efficient method for calculating electronic bound states in arbitrary one-dimensional quantum wells
de Aquino, V. M.; Iwamoto, H.; Dias, I. F. L.; Laureto, E.; da Silva, M. A. T.; da Silva, E. C. F.; Quivy, A. A.
2017-01-01
In the present paper it is demonstrated that the bound electronic states of multiple quantum wells structures may be calculated very efficiently by expanding their eigenstates in terms of the eigenfunctions of a particle in a box. The bound states of single and multiple symmetric or nonsymmetric wells are calculated within the single-band effective mass approximation. A comparison is then made between the results obtained for simple cases with exact calculations. We also apply our approach to a GaAs/AlGaAs multiple quantum well structure composed of forty periods each one with seven quantum wells. The method may be very useful to design narrow band quantum cascade photodetectors to work without applied bias in a photovoltaic mode. With the presented method the effects of a electric field may also be easily included which is very important if one desires study quantum well structures for application to the development of quantum cascade lasers. The advantages of the method are also presented.
Calculation of Excitonic Transitions in ZnO/MgZnO Quantum-Well Heterostructures
Institute of Scientific and Technical Information of China (English)
徐天宁; 吴惠桢; 邱东江; 陈乃波
2003-01-01
We calculate the excitonic transition energies and exciton binding energies in ZnO/MgxZn1-xO quantum-well heterostructures with Mg composition x varied from 0.08 to 0.36. The effect of the exciton-phonon interaction on the exciton binding energies is taken into account in the model. For the ZnO/Mg0.12Zn0.88O quantum-well structure, we compare the calculated result with the available experimental data at 5 K, and a good agreement is achieved. The excitonic transition energies at room temperature in ZnO/MgxZn1-xO quantum-well heterostructures are also calculated. The results show that when the well width exceeds 50 A, the quantum size effect is neglectable and the excitonic transition energies in ZnO/MgxZn1-xO (with x varied from 0.08 to 0.36)quantum-well heterostructures are close to the value of bulk ZnO. The maximum exciton binding energy as large as 121.1 meV is obtained for the well width of 12.5 A in the ZnO/Mg0.36Zn0.64O quantum-well heterostructures.
Cammi, Roberto
2015-11-15
A quantum chemical method for studying potential energy surfaces of reactive molecular systems at extreme high pressures is presented. The method is an extension of the standard Polarizable Continuum Model that is usually used for Quantum Chemical study of chemical reactions at a standard condition of pressure. The physical basis of the method and the corresponding computational protocol are described in necessary detail, and an application of the method to the dimerization of cyclopentadiene (up to 20 GPa) is reported.
Green's functions technique for calculating the emission spectrum in a quantum dot-cavity system
Directory of Open Access Journals (Sweden)
Edgar Arturo Gómez
2016-12-01
Full Text Available We introduce the Green's functions technique as an alternative theory to the quantum regression theorem formalism for calculating the two-time correlation functions in open quantum systems at the steady state. In order to investigate the potential of this theoretical approach, we consider a dissipative system composed of a single quantum dot inside a semiconductor cavity and the emission spectrum is computed due to the quantum dot as well as the cavity. We propose an algorithm based on the Green's functions technique for computing the emission spectrum that can easily be adapted to more complex open quantum systems. We found that the numerical results based on the Green's functions technique are in perfect agreement with the quantum regression theorem formalism. Moreover, it allows overcoming the inherent theoretical difficulties associated with the direct application of the quantum regression theorem in open quantum systems. Received: 6 September 2016, Accepted: 5 November 2016; Edited by: J. P. Paz; DOI: http://dx.doi.org/10.4279/PIP.080008 Cite as: E A Gómez, J D Hernández-Rivero, H Vinck-Posada, Papers in Physics 8, 080008 (2016
Burkatzki, M; Filippi, Claudia; Dolg, M
2008-10-28
We extend our recently published set of energy-consistent scalar-relativistic Hartree-Fock pseudopotentials by the 3d-transition metal elements, scandium through zinc. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. The pseudopotentials and the accompanying basis sets (VnZ with n=T,Q) are given in standard Gaussian representation and their parameter sets are presented. Coupled cluster, configuration interaction, and QMC studies are carried out for the scandium and titanium atoms and their oxides, demonstrating the good performance of the pseudopotentials. Even though the choice of pseudopotential form is motivated by QMC, these pseudopotentials can also be employed in other quantum chemical approaches.
A quantum chemical study on hydrogen radical reactions with methane and silane
Sato, Kota; Kojima, Kuniharu; Kawasaki, Masashi; Matsuzaki, Yoshio; Hirano, Tsuneo; Nakano, Masatake; Koinuma, Hideomi
1989-03-01
A quantum chemical study on the reaction of CH4 , CF4 , SiH4 , and SiF4 with a hydrogen radical is performed on the basis of an ab initio molecular orbital calculation to predict the photochemical reactivity of methane, silane, and their analogues. The transition state geometry of the reactions is determined by employing a 3-21G basis set. The total energies of reactant molecules at the initial, transition, and final states are calculated by employing a 6-31G** basis set. The exponential parts of the rate constants of these reactions determined from these energies on the basis of the transition state theory are in good agreement with the experimentally obtained relative rates of the reaction. The present calculation was consistent with the experimental results of photochemical reactions for methane and silane derivatives.
Clouds in Super-Earth Atmospheres: Chemical Equilibrium Calculations
Mbarek, Rostom; Kempton, Eliza M.-R.
2016-08-01
Recent studies have unequivocally proven the existence of clouds in super-Earth atmospheres. Here we provide a theoretical context for the formation of super-Earth clouds by determining which condensates are likely to form under the assumption of chemical equilibrium. We study super-Earth atmospheres of diverse bulk composition, which are assumed to form by outgassing from a solid core of chondritic material, following Schaefer & Fegley. The super-Earth atmospheres that we study arise from planetary cores made up of individual types of chondritic meteorites. They range from highly reducing to oxidizing and have carbon to oxygen (C:O) ratios that are both sub-solar and super-solar, thereby spanning a range of atmospheric composition that is appropriate for low-mass exoplanets. Given the atomic makeup of these atmospheres, we minimize the global Gibbs free energy of formation for over 550 gases and condensates to obtain the molecular composition of the atmospheres over a temperature range of 350-3000 K. Clouds should form along the temperature-pressure boundaries where the condensed species appear in our calculation. We find that the composition of condensate clouds depends strongly on both the H:O and C:O ratios. For the super-Earth archetype GJ 1214b, KCl and ZnS are the primary cloud-forming condensates at solar composition, in agreement with previous work. However, for oxidizing atmospheres, K2SO4 and ZnO condensates are favored instead, and for carbon-rich atmospheres with super-solar C:O ratios, graphite clouds appear. For even hotter planets, clouds form from a wide variety of rock-forming and metallic species.
Quantum Nuclear Pasta Calculations with Twisted Angular Boundary Conditions
Schuetrumpf, Bastian; Nazarewicz, Witold
2015-10-01
Nuclear pasta, expected to be present in the inner crust of neutron stars and core collapse supernovae, can contain a wide spectrum of different exotic shapes such as nuclear rods and slabs. There are also more complicated, network-like structures, the triply periodic minimal surfaces, already known e.g. in biological systems. These shapes are studied with the Hartree-Fock method using modern Skyrme forces. Furthermore twisted angular boundary conditions are utilized to reduce finite size effects in the rectangular simulation boxes. It is shown, that this improves the accuracy of the calculations drastically and additionally more insights into the mechanism of forming minimal surfaces can be gained.
Quantum Chemistry Calculations on the Interaction Between Kaolinite and Gold
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
The density function and discrete variation method (DFT-DVM) is used to study the interaction between kaolinite and gold. The correlation among the structure, chemical bond and stability is discussed. Several models are selected without gold and with gold in different directions and sites. The results show that the models with gold on the edge of kaolinite basal layer are more stable than those with gold above or under the layer, the models with gold near to ［AlO2(OH)4］ octahedra are more stable than those with gold near to the vacancy without aluminium. The interaction between gold and the surface ions of kaolinite is strong enough to form the surface complexes.
Afifi, Mahmoud S; Farag, Rabei S; Shaaban, Ibrahim A; Wilson, Lee D; Zoghaib, Wajdi M; Mohamed, Tarek A
2013-07-01
The infrared (4000-200 cm(-1)) spectrum for 4-amino-5-pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the (1)H and (13)C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the (1)H and (13)C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm(-1) (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.
Nonadiabatic quantum dynamics calculations for the N + NH --> N(2) + H reaction.
Yang, Huan; Hankel, M; Varandas, Antonio; Han, Keli
2010-09-01
Nonadiabatic quantum dynamics calculations on the two coupled potential energy surfaces (PESs) (1(2)A' and 2(2)A') and also adiabatic quantum calculations on the lowest adiabatic PES are reported for the title reaction. Reaction probabilities for total angular momenta, J, varying from 0 to 160, are calculated to obtain the integral cross section (ICS) for collision energies ranging from 0.05 to 1.0 eV. Calculations using both the close coupling and the Centrifugal Sudden (CS) approximation are carried out to evaluate the role of Coriolis coupling effects for this reaction. The results of the nonadiabatic calculations show that the nonadiabatic effects in the title reaction for the initial state of NH (v = 0, j = 0) could be neglected, at least in the collision energy range considered in this study.
Equation of State of Al Based on Quantum Molecular Dynamics Calculations
Minakov, Dmitry V.; Levashov, Pavel R.; Khishchenko, Konstantin V.
2011-06-01
In this work, we present quantum molecular dynamics calculations of the shock Hugoniots of solid and porous samples as well as release isentropes and values of isentropic sound velocity behind the shock front for aluminum. We use the VASP code with an ultrasoft pseudopotential and GGA exchange-correlation functional. Up to 108 particles have been used in calculations. For the Hugoniots of Al we solve the Hugoniot equation numerically. To calculate release isentropes, we use Zel'dovich's approach and integrate an ordinary differential equation for the temperature thus restoring all thermodynamic parameters. Isentropic sound velocity is calculated by differentiation along isentropes. The results of our calculations are in good agreement with experimental data. Thus, quantum molecular dynamics results can be effectively used for verification or calibration of semiempirical equations of state under conditions of lack of experimental information at high energy densities. This work is supported by RFBR, grants 09-08-01129 and 11-08-01225.
Multi channel quantum defect theory calculations of the Rydberg spectra of HCO
Douguet, Nicolas; Orel, Ann
2014-05-01
We present a first-principles theoretical study of the photoionization spectra of vibrationally autoionizing Rydberg states converging to excited states of HCO+. The clamped-nuclei scattering matrix, quantum defects parameters and transition dipole moments are explicitly calculated using the complex variational Kohn technique. The multi-channel quantum defect theory and vibrational frame transformation are then used to calculate the absorption spectrum. The results are compared with experimental data on double-resonance spectroscopy of the high Rydberg states of formyl radical. This work is supported by the DOE Office of Basic Energy Science and the National Science Foundation, Grant No's PHY-10-68785 and PHY-11-60611.
Analytic calculations of trial wave functions of the fractional quantum Hall effect on the sphere
Energy Technology Data Exchange (ETDEWEB)
Souza Batista, C.L. de [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil); Dingping Li [Perugia Univ. (Italy). Dipt. di Fisica
1996-07-01
We present a framework for the analytic calculations of the hierarchical wave functions and the composite fermion wave functions in the fractional quantum Hall effect on the sphere by using projective coordinates. Then we calculate the overlaps between these two wave functions at various fillings and small numbers of electrons. We find that the overlaps are most equal to one. This gives a further evidence that two theories of the fractional quantum Hall effect, the hierarchical theory, are physically equivalent. (author). 31 refs., 2 tabs.
Improved transfer matrix methods for calculating quantum transmission coefficient.
Biswas, Debabrata; Kumar, Vishal
2014-07-01
Methods for calculating the transmission coefficient are proposed, all of which arise from improved nonreflecting WKB boundary conditions at the edge of the computational domain in one-dimensional geometries. In the first, the Schrödinger equation is solved numerically, while the second is a transfer matrix (TM) algorithm where the potential is approximated by steps, but with the first and last matrix modified to reflect the new boundary condition. Both methods give excellent results with first-order WKB boundary conditions. The third uses the transfer matrix method with third-order WKB boundary conditions. For the parabolic potential, the average error for the modified third-order TM method reduces by factor of 4100 over the unmodified TM method.
Energy Technology Data Exchange (ETDEWEB)
Alam, T.M.
1998-09-01
The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.
Auxiliary-field-based trial wave functions in quantum Monte Carlo calculations
Chang, Chia-Chen; Rubenstein, Brenda M.; Morales, Miguel A.
2016-12-01
Quantum Monte Carlo (QMC) algorithms have long relied on Jastrow factors to incorporate dynamic correlation into trial wave functions. While Jastrow-type wave functions have been widely employed in real-space algorithms, they have seen limited use in second-quantized QMC methods, particularly in projection methods that involve a stochastic evolution of the wave function in imaginary time. Here we propose a scheme for generating Jastrow-type correlated trial wave functions for auxiliary-field QMC methods. The method is based on decoupling the two-body Jastrow into one-body projectors coupled to auxiliary fields, which then operate on a single determinant to produce a multideterminant trial wave function. We demonstrate that intelligent sampling of the most significant determinants in this expansion can produce compact trial wave functions that reduce errors in the calculated energies. Our technique may be readily generalized to accommodate a wide range of two-body Jastrow factors and applied to a variety of model and chemical systems.
Dracínský, Martin; Pohl, Radek; Slavetínská, Lenka; Budesínský, Milos
2010-09-01
A series of model sulfides was oxidized in the NMR sample tube to sulfoxides and sulfones by the stepwise addition of meta-chloroperbenzoic acid in deuterochloroform. Various methods of quantum chemical calculations have been tested to reproduce the observed (1)H and (13)C chemical shifts of the starting sulfides and their oxidation products. It has been shown that the determination of the energy-minimized conformation is a very important condition for obtaining realistic data in the subsequent calculation of the NMR chemical shifts. The correlation between calculated and observed chemical shifts is very good for carbon atoms (even for the 'cheap' DFT B3LYP/6-31G* method) and somewhat less satisfactory for hydrogen atoms. The calculated chemical shifts induced by oxidation (the Delta delta values) agree even better with the experimental values and can also be used to determine the oxidation state of the sulfur atom (-S-, -SO-, -SO(2)-).
Bouhali, I.; Bezzaouia, S.; Telmini, M.; Jungen, Ch.
2016-08-01
Variational ab initio R -matrix theory combined with generalized multichannel quantum defect theory is used to calculate singly excited Rydberg states of the hydrohelium molecular ion, HeH+, for Σ,3+1,Π,31,Δ,31,Φ,31, and Γ,31 symmetry. Bound levels are calculated for n values up to n ≈10 , and continuum states up to ≈3 eV above the HeH2 + threshold. The calculations span the range of internuclear distances R from 1 to 5 bohrs. The present work follows a preliminary study on the Δ,31 states of HeH+ [Bouhali, Bezzaouia, Telmini, and Jungen, EPJ Web Conf. 84, 04004 (2015), 10.1051/epjconf/20158404004] which was also based on R -matrix theory. Further—although limited to rather small R values—the present work extends the recent ab initio computations of Jungen and Jungen [Mol. Phys. 113, 2333 (2015), 10.1080/00268976.2015.1040094] to higher excitation energies which are not accessible to standard quantum-chemical methods. Where a comparison with the calculations of Jungen and Jungen and other older results can be made, namely for n ≤5 , very good agreement with previous ab initio results is obtained.
Molecular docking, spectroscopic studies and quantum calculations on nootropic drug.
Uma Maheswari, J; Muthu, S; Sundius, Tom
2014-04-05
A systematic vibrational spectroscopic assignment and analysis of piracetam [(2-oxo-1-pyrrolidineacetamide)] have been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G++(d,p) basis set. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, and harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption wavelengths λmax were determined by the time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. Molecular docking studies have been carried out in the active site of piracetam by using Argus Lab. In addition, the potential energy surface, HOMO and LUMO energies, first-order hyperpolarizability and the molecular electrostatic potential have been computed.
Directory of Open Access Journals (Sweden)
Claudio Amovilli
2016-02-01
Full Text Available In this work, we present a simple decomposition scheme of the Kohn-Sham optimized orbitals which is able to provide a reduced basis set, made of localized polycentric orbitals, specifically designed for Quantum Monte Carlo. The decomposition follows a standard Density functional theory (DFT calculation and is based on atomic connectivity and shell structure. The new orbitals are used to construct a compact correlated wave function of the Slater–Jastrow form which is optimized at the Variational Monte Carlo level and then used as the trial wave function for a final Diffusion Monte Carlo accurate energy calculation. We are able, in this way, to capture the basic information on the real system brought by the Kohn-Sham orbitals and use it for the calculation of the ground state energy within a strictly variational method. Here, we show test calculations performed on some small selected systems to assess the validity of the proposed approach in a molecular fragmentation, in the calculation of a barrier height of a chemical reaction and in the determination of intermolecular potentials. The final Diffusion Monte Carlo energies are in very good agreement with the best literature data within chemical accuracy.
Semenov, Alexander; Babikov, Dmitri
2014-01-16
For computational treatment of rotationally inelastic scattering of molecules, we propose to use the mixed quantum/classical theory, MQCT. The old idea of treating translational motion classically, while quantum mechanics is used for rotational degrees of freedom, is developed to the new level and is applied to Na + N2 collisions in a broad range of energies. Comparison with full-quantum calculations shows that MQCT accurately reproduces all, even minor, features of energy dependence of cross sections, except scattering resonances at very low energies. The remarkable success of MQCT opens up wide opportunities for computational predictions of inelastic scattering cross sections at higher temperatures and/or for polyatomic molecules and heavier quenchers, which is computationally close to impossible within the full-quantum framework.
Quantum calculations for photodetachment cross sections of H- in an inhomogeneous electric field
Institute of Scientific and Technical Information of China (English)
Wu Xiao-Qing; Du Meng-Li; Zhao Hai-Jun
2012-01-01
We calculate the photodetachment cross sections of Hˉ in a gradient electric field based on traditional quantum approach.The system provides a rare example that the formulas for the cross sections can be explicitly derived by both the quantum approach and closed-orbit theory.The quantum results are compared with those of the closed-orbit theory.The correct phase values in the closed-orbit theory are essential and necessary to produce accurate cross sections.Our quantum results remove some previous ambiguities in assigning the phase values in the closed-orbit theory (G.C.Yang and M.L.Du 2007 Phys.Rev.A 75 029904E).
Balachandran, V; Rajeswari, S; Lalitha, S
2014-04-24
The FT-IR and FT-Raman spectra of 4-(dimethylamino) pyridine (4DMAP) have been recorded in the region 4000-500 cm(-1)and 3500-100 cm(-1). Quantum chemical calculations of energy, geometry and vibrational wavenumbers of 4DMAP were carried out by using ab initio HF and density functional theory (DFT/B3LYP) with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The harmonic vibrational wavenumbers were calculated and the scaled wavenumbers have been compared with the experimental FT-IR and FT-Raman spectra. The quantum chemical parameters have been computed from the HOMO-LUMO energy values. Temperature dependence thermodynamic parameters and magnetic properties of the title compound have been analyzed. Using NBO analysis the stability of the molecule arising from hyper-conjugative interactions, charge delocalization has been analyzed. The first-order hyper-polarizability (β) values of the title molecule were computed by B3LYP method. Finally the theoretically spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed which show good agreement with recorded spectra.
Quantum measurement corrections to chemically induced dynamic nuclear polarization
Kominis, I K
2013-01-01
Chemically induced dynamic nuclear polarization has emerged as a universal signature of spin order in photosynthetic reaction centers. Such polarization, significantly enhanced above thermal equilibrium, is known to result from the nuclear spin sorting inherent in the radical pair mechanism underlying long-lived charge-separated states in photosynthetic reaction centers. We will here show that the recently understood fundamental quantum dynamics of radical-ion-pair reactions open up a new and completely unexpected venue towards obtaining CIDNP signals. The fundamental decoherence mechanism inherent in the recombination process of radical pairs is shown to produce nuclear spin polarizations on the order of $10^4$ times or more higher than thermal equilibrium values at low fields relevant to natural photosynthesis in earth's magnetic field. This opens up the possibility of a fundamentally new exploration of the biological significance of high nuclear polarizations in photosynthesis.
Quantum chemical study on asymmetric catalysis reduction of imine
Institute of Scientific and Technical Information of China (English)
LI; Ming; (李明); TIAN; Anmin; (田安民)
2003-01-01
The quantum chemical method is employed to study the enantioselective reduction of imine with borane catalyzed by chiral oxazaborolidine. All the structures are optimized completely at the B3LYP/6-31G(d) level. The catalysis property of oxazaborolidine is notable. The reduction goes mainly through the formations of the catalyst-borane adduct, the catalyst-borane-imine adduct, and the catalyst-amidoborane adduct and the dissociation of the catalyst-amidoborane adduct with the regeneration of the catalyst. The controlling step for the reduction is the dissociation of the catalyst-amidoborane adduct. The main reduced product predicted theoretically is (R )-sec- ondary amine, which is in agreement with the experiment.
Directory of Open Access Journals (Sweden)
Isabella Natali Sora
2012-01-01
Full Text Available Quantum mechanics density functional calculations provided gas-phase electron distributions and proton affinities for several mono- and diaza[5]helicenes; computational results, together with experimental data concerning crystal structures and propensity to methylation of the nitrogen atom(s, provide a basis for designing azahelicene complexes with transition metal ions.
Monte Carlo calculation of quantum tunneling in the dilute instanton limit
Cross, M. C.
1986-01-01
A new approach for estimating small quantum tunneling rates by Monte Carlo calculation is proposed and demonstrated on a simple one-dimensional model. The application to many-body situations such as atomic exchange in solid 3He is discussed.
Young’s modulus calculations for cellulose Iß by MM3 and quantum mechanics
Quantum mechanics (QM) and molecular mechanics (MM) calculations were performed to elucidate Young’s moduli for a series of cellulose Iß models. Computations using the second generation empirical force field MM3 with a disaccharide cellulose model, 1,4'-O-dimethyl-ß-cellobioside (DMCB), and an analo...
Durrant, Marcus C
2007-01-01
The process of gene-based molecular evolution has been simulated in silico by using massively parallel density functional theory quantum calculations, coupled with a genetic algorithm, to test for fitness with respect to a target chemical reaction in populations of genetically encoded molecules. The goal of this study was the identification of transition-metal complexes capable of mediating a known reaction, namely the cleavage of N(2) to give the metal nitride. Each complex within the search space was uniquely specified by a nanogene consisting of an eight-digit number. Propagation of an individual nanogene into successive generations was determined by the fitness of its phenotypic molecule to perform the target reaction and new generations were created by recombination and mutation of surviving nanogenes. In its simplest implementation, the quantum-directed genetic algorithm (QDGA) quickly located a local minimum on the evolutionary fitness hypersurface, but proved incapable of progressing towards the global minimum. A strategy for progressing beyond local minima consistent with the Darwinian paradigm by the use of environmental variations coupled with mass extinctions was therefore developed. This allowed for the identification of nitriding complexes that are very closely related to known examples from the chemical literature. Examples of mutations that appear to be beneficial at the genetic level but prove to be harmful at the phenotypic level are described. As well as revealing fundamental aspects of molecular evolution, QDGA appears to be a powerful tool for the identification of lead compounds capable of carrying out a target chemical reaction.
Quantum chemical analysis for the formation of glycine in the interstellar medium
Institute of Scientific and Technical Information of China (English)
Amresh Singh; Shivani; Alka Misra; Poonam Tandon
2013-01-01
Glycine (C2H5NO2) was the first amino acid to be detected in space by the stardust space probe in Comet Wild2,and is used by living organisms to make proteins.We discuss three different reaction paths for the formation of glycine in interstellar space from some simpler molecules detected in the interstellar medium.The possibility of the formation of glycine in interstellar space is considered by radicalradical and radical-molecule interaction schemes using quantum chemical calculations with density functional theory at the B3LYP/6-31G (d,p) level.In the chemical pathways we discuss,a few reactions are found to be totally exothermic and barrierless while others are endothermic with a very small reaction barrier,thus giving rise to a high probability of forming glycine in interstellar space.
Quantum-chemical examination of interaction of cytostatic-fluorouracil with deoxyribonucleic acids
Yuldasheva, Gulnara; Zhidomirov, Georgii M.
Within the framework of semiempirical method of quantum chemical PM3, the possibility of formation of paired stack structures under interaction of fluorouracil with pyrimidine and purine nitrogenous bases of nucleotides has been examined. Possible mechanism of transformation of 2-deoxyuridine-5-monophosphate into metabolite-5-fluorin-2-deoxyuridine-5-monophosphate has been given. The calculations that were made allow to suppose that biotransformation of 5-FU in 5-fluorin-2-deoxyuridine-5-monophosphate, most likely, is carried out not in free nucleotides, but in the structure of DNA in two nucleotide triplets UUC and UGU, including the case when directly two nucleotides of deoxyuridine monophosphate, are transformed into 5-fluorin-2-deoxyuridine-5-monophosphate. Cytostatic ability of 5-FU is increased by its capacity to be selectively embedded into nucleotide triplets creating new chemical compounds that violate matrix RNA formation and accordingly violate protein synthesis.0
Jiang, Jun; Kula, Mathias; Luo, Yi
2006-01-01
A generalized quantum chemical approach for electron transport in molecular devices is developed. It allows one to treat devices where the metal electrodes and the molecule are either chemically or physically bonded on equal footing. An extension to include the vibration motions of the molecule has also been implemented which has produced the inelastic electron-tunneling spectroscopy of molecular electronics devices with unprecedented accuracy. Important information about the structure of the molecule and of metal-molecule contacts that are not accessible in the experiment are revealed. The calculated current-voltage (I-V) characteristics of different molecular devices, including benzene-1,4-dithiolate, octanemonothiolate [H(CH2)8S], and octanedithiolate [S(CH2)8S] bonded to gold electrodes, are in very good agreement with experimental measurements.
Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira
The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.
Quantum chemical analysis of potential anti-Parkinson agents
Indian Academy of Sciences (India)
Nima Razzaghi-Asl; Sara Shahabipour; Ahmad Ebadi; Azam Bagheri
2015-07-01
Monoamine oxidases (MAOs) are amine oxidoreductase falvoenzymes that belong to the integral proteins of the outer mitochondrial membrane. MAO exists in two distinct isoforms; MAO-A and MAO-B. Inhibition of MAO-A and MAO-B is important for developing antidepressant and antiparkinson agents, respectively. In the light of the above explanations, detailed structure binding relationship studies on the intermolecular binding components of MAO-B complexes may unravel the way toward developing novel anti-Parkinson agents. In the present contribution, intermolecular binding pattern for a series of experimentally validated 3-arylcoumarin MAO-B inhibitors (1–9) have been elucidated via molecular docking and density functional theory (DFT) calculations. Intermolecular binding energy components could not be analyzed by docking and due to this limitation, quantum mechanical (QM) calculations including functional B3LYP in association with split valence basis set (Def2-SVP) were applied to estimate the ligand-residue binding energies in the MAO-B active site. Moreover; results were interpreted in terms of calculated polarization effects that were induced by individual amino acids of the MAO-B active site. The results of the present study provide an approach to pharmacophore-based modification within the 3-arylcoumarin scaffold for potent MAO-B inhibitors.
Ion chemistry in the early universe: revisiting the role of HeH+ with new quantum calculations
Bovino, Stefano; Gianturco, Francesco A; Galli, Daniele
2011-01-01
The role of HeH+ has been newly assessed with the aid of newly calculated rates which use entirely ab initio methods, thereby allowing us to compute more accurately the relevant abundances within the global chemical network of the early universe. A comparison with the similar role of the ionic molecule LiH+ is also presented. Quantum calculations have been carried out for the gas-phase reaction of HeH+ with H atoms with our new in-house code, based on the negative imaginary potential method. Integral cross sections and reactive rate coefficients obtained under the general conditions of early universe chemistry are presented and discussed. With the new reaction rate, the abundance of HeH+ in the early universe is more than one order of magnitude larger than in previous studies. Our more accurate findings further buttress the possibility to detect cosmological signatures of HeH+.
Quantum calculations of H2-H2 collisions: from ultracold to thermal energies
Quéméner, Goulven
2008-01-01
We present quantum dynamics of collisions between two para-H2 molecules from low (1 mK) to high collision energies (1 eV). The calculations are carried out using a quantum scattering code that solves the time-independent Schrodinger equation in its full dimensionality without any decoupling approximations. The six-dimensional potential energy surface for the H4 system developed by Boothroyd et al. [J. Chem. Phys. 116, 666 (2002)] is used in the calculations. Elastic, inelastic and state-to-state cross sections as well as rate coefficients from T = 1 K to 400 K obtained from our calculations are compared with available experimental and theoretical results. Overall, good agreement is obtained with previous studies.
Quantum and Semiclassical Calculations of Cold Atom Collisions in Light Fields
Suominen, K A; Tuvi, I; Burnett, K; Julienne, P S
1998-01-01
We derive and apply an optical Bloch equation (OBE) model for describing collisions of ground and excited laser cooled alkali atoms in the presence of near-resonant light. Typically these collisions lead to loss of atoms from traps. We compare the results obtained with a quantum mechanical complex potential treatment, semiclassical Landau-Zener models with decay, and a quantum time-dependent Monte-Carlo wave packet (MCWP) calculation. We formulate the OBE method in both adiabatic and diabatic representations. We calculate the laser intensity dependence of collision probabilities and find that the adiabatic OBE results agree quantitatively with those of the MCWP calculation, and qualitatively with the semiclassical Landau-Zener model with delayed decay, but that the complex potential method or the traditional Landau-Zener model fail in the saturation limit.
Variational Calculations of Neutral Bound Excitons in GaAs Quantum-Well Wires
Institute of Scientific and Technical Information of China (English)
LIU Jian-Jun; DI Bing; YANG Guo-Chen; LI Shu-Shen
2004-01-01
@@ The binding energy of an exciton bound to a neutral donor (D0, X) in GaAs quantum-well wires is calculated variationally as a function of the wire width for different positions of the impurity inside the wire by using a two-parameter wavefunction. There is no artificial parameter added in our calculation. The results we have obtained show that the binding energies are closely correlated to the sizes of the wire, the impurity position, and also that their magnitudes are greater than those in the two-dimensional quantum wells compared. In addition,we also calculate the average interparticle distance as a function of the wire width. The results are discussed in detail.
Calculation of quantum discord for qubit-qudit or N qubits
vinjanampathy, sai
2011-01-01
Quantum discord, a kind of quantum correlation, is defined as the difference between quantum mutual information and classical correlation in a bipartite system. It has been discussed so far for small systems with only a few independent parameters. We extend here to a much broader class of states when the second party is of arbitrary dimension d, so long as the first, measured, party is a qubit. We present two formulae to calculate quantum discord, the first relating to the original entropic definition and the second to a recently proposed geometric distance measure which leads to an analytical formulation. The tracing over the qubit in the entropic calculation is reduced to a very simple prescription. And, when the d-dimensional system is a so-called X state, the density matrix having non-zero elements only along the diagonal and anti-diagonal so as to appear visually like the letter X, the entropic calculation can be carried out analytically. Such states of the full bipartite qubit-qudit system may be named ...
The Study of Alcoholysis of 1,2-Thiazetidine-1,1-dioxide with Quantum Chemical Method
Institute of Scientific and Technical Information of China (English)
Mao Xia HE; Feng ZHU; Da Cheng FENG; Zheng Ting CAI
2004-01-01
The alcoholysis mechanism of 1,2-thiazetidine-1,1-dioxide with methanol, in which the relatively stable product is sulfonate ester, has been investigated by quantum chemical method. Our calculations indicate the reaction for alcoholysis of 1,2-thiazetidine-1,1-dioxide proceeds via two possible mechanisms: concerted and stepwise. In the stepwise mechanism, two possible reaction pathways can be followed while only one possible reaction pathway can be followed in the concerted mechanism.
Gonoskov, Ivan; Marklund, Mattias
2016-05-01
We propose and develop a general method of numerical calculation of the wave function time evolution in a quantum system which is described by Hamiltonian of an arbitrary dimensionality and with arbitrary interactions. For this, we obtain a general n-order single-step propagator in closed-form, which could be used for the numerical solving of the problem with any prescribed accuracy. We demonstrate the applicability of the proposed approach by considering a quantum problem with non-separable time-dependent Hamiltonian: the propagation of an electron in focused electromagnetic field with vortex electric field component.
Helping Students Develop a Critical Attitude towards Chemical Process Calculations.
de Nevers, Noel; Seader, J. D.
1992-01-01
Discusses the use of computer-assisted programs that allow chemical engineering students to study textbook thermodynamics problems from different perspectives, including the classical graphical method, while utilizing more than one property correlation and/or operation model so that comparisons can be made and sensitivities determined more…
Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H
2013-01-01
We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...
Comparison of Hugoniots calculated for aluminum in the framework of three quantum-statistical models
Kadatskiy, Maxim A
2015-01-01
The results of calculations of thermodynamic properties of aluminum under shock compression in the framework of the Thomas--Fermi model, the Thomas--Fermi model with quantum and exchange corrections and the Hartree--Fock--Slater model are presented. The influences of the thermal motion and the interaction of ions are taken into account in the framework of three models: the ideal gas, the one-component plasma and the charged hard spheres. Calculations are performed in the pressure range from 1 to $10^7$ GPa. Calculated Hugoniots are compared with available experimental data.
Comparison of Hugoniots calculated for aluminum in the framework of three quantum-statistical models
Kadatskiy, M. A.; Khishchenko, K. V.
2015-11-01
The results of calculations of thermodynamic properties of aluminum under shock compression in the framework of the Thomas-Fermi model, the Thomas-Fermi model with quantum and exchange corrections and the Hartree-Fock-Slater model are presented. The influences of the thermal motion and the interaction of ions are taken into account in the framework of three models: the ideal gas, the one-component plasma and the charged hard spheres. Calculations are performed in the pressure range from 1 to 107 GPa. Calculated Hugoniots are compared with available experimental data.
DEFF Research Database (Denmark)
van Harrevelt, Rob; Honkala, Johanna Karoliina; Nørskov, Jens Kehlet
2005-01-01
Quantum-mechanical calculations of the reaction rate for dissociative adsorption of N-2 on stepped Ru(0001) are presented. Converged six-dimensional quantum calculations for this heavy-atom reaction have been performed using the multiconfiguration time-dependent Hartree method. A potential...
Chemical physics: Quantum control of light-induced reactions
Chandler, David W.
2016-07-01
An investigation of how ultracold molecules are broken apart by light reveals surprising, previously unobserved quantum effects. The work opens up avenues of research in quantum optics. See Letter p.122
Chemically reacting supersonic flow calculation using an assumed PDF model
Farshchi, M.
1990-01-01
This work is motivated by the need to develop accurate models for chemically reacting compressible turbulent flow fields that are present in a typical supersonic combustion ramjet (SCRAMJET) engine. In this paper the development of a new assumed probability density function (PDF) reaction model for supersonic turbulent diffusion flames and its implementation into an efficient Navier-Stokes solver are discussed. The application of this model to a supersonic hydrogen-air flame will be considered.
Zakharenko, Olena; Aviles Moreno, Juan-Ramon; Imane, Haykal; Motiyenko, R. A.; Huet, T. R.; Pirali, Olivier
2014-06-01
Methacrolein, CH_2=C(CH_3)CHO or MAC, is an important atmospheric molecule because it is a major product of the isoprene-OH reaction. Meanwhile the spectroscopic information on MAC is very scarse. On the theoretical side, we have performed quantum calculations at different levels of theory (DFT and ab initio) to model the structure of the two conformers, the large amplitude motion associated with the methyl top, and the anharmonic vibrational structure. On the experimental side, we have at first characterized the millimeter-wave spectrum of MAC in the 150-465 GHz range using the Lille frequency multiplication chain spectrometer. In particular the ground state has been analyzed up to J, K_a = 37, 17 and the first excited states are currently investigated. Secondly, FTIR spectra have been recorded on the AILES beamline of SOLEIL using a long path cell, between 30 and 3500 wn at medium resolution (0.5 wn). A few bands of atmospheric interest have also been recorded at higher resolution (0.001 wn). We will report the details of the vibrational analysis, as well as the molecular parameters derived from the analysis of the high resolution spectrum of the c-type band located around 930 wn. Support from the French Laboratoire d'Excellence CaPPA (Chemical and Physical Properties of the Atmosphere) through contract ANR-10-LABX-0005 of the Programme d'Investissements d'Avenir is acknowledged. The experiment on the AILES beam-line of the synchrotron SOLEIL was performed under project number 20130192. M. Suzuki and K. Kozima, J. Molec. Spectrosc. 38 (1971) 314 J. R. Durig, J. Qiu, B. Dehoff and T. S. Little, Spectrochimica Acta 42A (1986) 89
Self-consistent calculations of optical properties of type I and type II quantum heterostructures
Shuvayev, Vladimir A.
In this Thesis the self-consistent computational methods are applied to the study of the optical properties of semiconductor nanostructures with one- and two-dimensional quantum confinements. At first, the self-consistent Schrodinger-Poisson system of equations is applied to the cylindrical core-shell structure with type II band alignment without direct Coulomb interaction between carriers. The electron and hole states and confining potential are obtained from a numerical solution of this system. The photoluminescence kinetics is theoretically analyzed, with the nanostructure size dispersion taken into account. The results are applied to the radiative recombination in the system of ZnTe/ZnSe stacked quantum dots. A good agreement with both continuous wave and time-resolved experimental observations is found. It is shown that size distribution results in the photoluminescence decay that has essentially non-exponential behavior even at the tail of the decay where the carrier lifetime is almost the same due to slowly changing overlap of the electron and hole wavefunctions. Also, a model situation applicable to colloidal core-shell nanowires is investigated and discussed. With respect to the excitons in type I quantum wells, a new computationally efficient and flexible approach of calculating the characteristics of excitons, based on a self-consistent variational treatment of the electron-hole Coulomb interaction, is developed. In this approach, a system of self-consistent equations describing the motion of an electron-hole pair is derived. The motion in the growth direction of the quantum well is separated from the in-plane motion, but each of them occurs in modified potentials found self-consistently. This approach is applied to a shallow quantum well with the delta-potential profile, for which analytical expressions for the exciton binding energy and the ground state eigenfunctions are obtained, and to the quantum well with the square potential profile with several
Arjunan, V.; Santhanam, R.; Marchewka, M. K.; Mohan, S.; Yang, Haifeng
2015-11-01
Tapentadol is a novel opioid pain reliever drug with a dual mechanism of action, having potency between morphine and tramadol. Quantum chemical calculations have been carried out for tapentadol hydrochloride (TAP.Cl) to determine the properties. The geometry is optimised and the structural properties of the compound were determined from the optimised geometry by B3LYP method using 6-311++G(d,p), 6-31G(d,p) and cc-pVDZ basis sets. FT-IR and FT-Raman spectra are recorded in the solid phase in the region of 4000-400 and 4000-100 cm-1, respectively. Frontier molecular orbital energies, LUMO-HOMO energy gap, ionisation potential, electron affinity, electronegativity, hardness and chemical potential are also calculated. The stability of the molecule arising from hyperconjugative interactions and charge delocalisation has been analysed using NBO analysis. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule are analysed.
Zhang, Dawei
2017-03-01
Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems.
Zhang, Dawei
2017-01-01
Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems. PMID:28300179
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.
"Shut up and calculate": the available discursive positions in quantum physics courses
Johansson, Anders; Andersson, Staffan; Salminen-Karlsson, Minna; Elmgren, Maja
2016-08-01
Educating new generations of physicists is often seen as a matter of attracting good students, teaching them physics and making sure that they stay at the university. Sometimes, questions are also raised about what could be done to increase diversity in recruitment. Using a discursive perspective, in this study of three introductory quantum physics courses at two Swedish universities, we instead ask what it means to become a physicist, and whether certain ways of becoming a physicist and doing physics is privileged in this process. Asking the question of what discursive positions are made accessible to students, we use observations of lectures and problem solving sessions together with interviews with students to characterize the discourse in the courses. Many students seem to have high expectations for the quantum physics course and generally express that they appreciate the course more than other courses. Nevertheless, our analysis shows that the ways of being a "good quantum physics student" are limited by the dominating focus on calculating quantum physics in the courses. We argue that this could have negative consequences both for the education of future physicists and the discipline of physics itself, in that it may reproduce an instrumental "shut up and calculate"-culture of physics, as well as an elitist physics education. Additionally, many students who take the courses are not future physicists, and the limitation of discursive positions may also affect these students significantly.
Uncertainty quantification for quantum chemical models of complex reaction networks.
Proppe, Jonny; Husch, Tamara; Simm, Gregor N; Reiher, Markus
2016-12-22
For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.
[Study of quantum-pharmacological chemical characteristics of quercetin].
Zahorodnyĭ, M I
2007-01-01
It was established in the previous studies that quercetin prevented the development and caused faster regression of ulcers, petechia and anabroses in rats, which were induced by diclofenac taking. In the group of patients taking diclofenac together with quercetin, the ulcers and dyspeptic events were less found. The application of quercetin normalizes the function and metabolism of cartilage tissue of rabbits with an experimental osteoarthrosis and in patients with osteoartrosis. Quantum-chemical properties of molecule quercetin were studied using the methods of molecular mechanics MM+ and ab initio 6-31G*, and also semiempirical method. The following indices were investigated: distance between atoms (A), the distribution of electronic density of only external valency electrons, distribution of electrostatic potential; common energy of the exertion of molecule (kkal/mmol); binding energy (kkal/mmol); electron energy (kkal/mmol); energy of nucleus-nucleus interaction (kkal/mmol); formation heat (kkal/mmol); atomic charge (eB); value of the dipole moment of molecule (D); localization and energy of highest occupied orbital (HOMO) and the lowest unoccupied (LUMO) molecular orbital (eB) of quercetin miolecule; the value of absolute rigidity of chemical structure of bioflavonoid. It was shown, that bioflavonoid quercetin belongs to mild reagents, has nucleophilic properties, can react with alkaline, unsaturated and aromatic compounds,. Polar substitutes in the quercetine molecule influence on the distribution of superficial valency electrons and localization of HOMO and LUMO. The energy value of quercetin LUMO enables us to refer quercetine to the reducing agent and it is illustrated by antioxidant properties of this medicine.
VARIATIONAL CALCULATION ON GROUND-STATE ENERGY OF BOUND POLARONS IN PARABOLIC QUANTUM WIRES
Institute of Scientific and Technical Information of China (English)
WANG ZHUANG-BING; WU FU-LI; CHEN QING-HU; JIAO ZHENG-KUAN
2001-01-01
Within the framework of Feynman path-integral variational theory, we calculate the ground-state energy of a polaron in parabolic quantum wires in the presence of a Coulomb potential. It is shown that the polaronic correction to the ground-state energy is more sensitive to the electron-phonon coupling constant than the Coulomb binding parameter,and it increases monotonically with decreasing effective wire radius. Moreover, compared to the results obtained by Feynman Haken variational path-integral theory, we obtain better results within the Feynman path-integral variational approach (FV approach). Applying our calculation to several polar semiconductor quantum wires, we find that the polaronic correction can be considerably large.
Protein structure refinement using a quantum mechanics-based chemical shielding predictor
DEFF Research Database (Denmark)
Bratholm, Lars Andersen; Jensen, Jan Halborg
2017-01-01
The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor...... of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic...
Tuning the Emission Energy of Chemically Doped Graphene Quantum Dots
Directory of Open Access Journals (Sweden)
Noor-Ul-Ain
2016-11-01
Full Text Available Tuning the emission energy of graphene quantum dots (GQDs and understanding the reason of tunability is essential for the GOD function in optoelectronic devices. Besides material-based challenges, the way to realize chemical doping and band gap tuning also pose a serious challenge. In this study, we tuned the emission energy of GQDs by substitutional doping using chlorine, nitrogen, boron, sodium, and potassium dopants in solution form. Photoluminescence data obtained from (Cl- and N-doped GQDs and (B-, Na-, and K-doped GQDs, respectively exhibited red- and blue-shift with respect to the photoluminescence of the undoped GQDs. X-ray photoemission spectroscopy (XPS revealed that oxygen functional groups were attached to GQDs. We qualitatively correlate red-shift of the photoluminescence with the oxygen functional groups using literature references which demonstrates that more oxygen containing groups leads to the formation of more defect states and is the reason of observed red-shift of luminescence in GQDs. Further on, time resolved photoluminescence measurements of Cl- and N-GQDs demonstrated that Cl substitution in GQDs has effective role in radiative transition whereas in N-GQDs leads to photoluminescence (PL quenching with non-radiative transition to ground state. Presumably oxidation or reduction processes cause a change of effective size and the bandgap.
Calculation rule for Aoyama-Tamra's prescription for path integral with quantum tunneling
Suzuki, H
1995-01-01
We derive a simple calculation rule for Aoyama--Tamra's prescription for path integral with degenerated potential minima. Non-perturbative corrections due to the restricted functional space (fundamental region) can systematically be computed with this rule. It becomes manifest that the prescription might give Borel summable series for finite temperature (or volume) system with quantum tunneling, while the advantage is lost at zero temperature (or infinite volume) limit.
STUDY OF GRAFT SITES IN EPOXY GRAFT COPOLYMERS BY QUANTUM CHEMISTRY CALCULATIONS
Institute of Scientific and Technical Information of China (English)
Song Chen; Xiao-yu Li
2009-01-01
Exploration and characterization of grafting productions by experimental methods are often cumbersome or sometimes impossible. Therefore, quantum chemistry calculations were performed to characterize the graft sites of epoxy resin. According to the Gibbs free energy criterion of the second law of thermodynamic, the reported graft sites were confirmed, and more important, some unreported graft sites were found. In addition, method of increasing the number of graft sites was studied in this article.
Combined spectroscopic and quantum chemical studies of ezetimibe
Prajapati, Preeti; Pandey, Jaya; Shimpi, Manishkumar R.; Srivastava, Anubha; Tandon, Poonam; Velaga, Sitaram P.; Sinha, Kirti
2016-12-01
Ezetimibe (EZT) is a hypocholesterolemic agent used for the treatment of elevated blood cholesterol levels as it lowers the blood cholesterol by blocking the absorption of cholesterol in intestine. Study aims to combine experimental and computational methods to provide insights into the structural and vibrational spectroscopic properties of EZT which is important for explaining drug substance physical and biological properties. Computational study on molecular properties of ezetimibe is presented using density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set. A detailed vibrational assignment has been done for the observed IR and Raman spectra of EZT. In addition to the conformational study, hydrogen bonding and molecular docking studies have been also performed. For conformational studies, the double well potential energy curves have been plotted for the rotation around the six flexible bonds of the molecule. UV absorption spectrum was examined in methanol solvent and compared with calculated one in solvent environment (IEF-PCM) using TD-DFT/6-31G basis set. HOMO-LUMO energy gap of both the conformers have also been calculated in order to predict its chemical reactivity and stability. The stability of the molecule was also examined by means of natural bond analysis (NBO) analysis. To account for the chemical reactivity and site selectivity of the molecules, molecular electrostatic potential (MEPS) map has been plotted. The combination of experimental and calculated results provide an insight into the structural and vibrational spectroscopic properties of EZT. In order to give an insight for the biological activity of EZT, molecular docking of EZT with protein NPC1L1 has been done.
Chemical Compass Model for Avian Magnetoreception as a Quantum Coherent Device
Cai, Jianming; Plenio, Martin B.
2013-12-01
It is known that more than 50 species use the Earth’s magnetic field for orientation and navigation. Intensive studies, particularly behavior experiments with birds, provide support for a chemical compass based on magnetically sensitive free radical reactions as a source of this sense. However, the fundamental question of how quantum coherence plays an essential role in such a chemical compass model of avian magnetoreception yet remains controversial. Here, we show that the essence of the chemical compass model can be understood in analogy to a quantum interferometer exploiting global quantum coherence rather than any subsystem coherence. Within the framework of quantum metrology, we quantify global quantum coherence and correlate it with the function of chemical magnetoreception. Our results allow us to understand and predict how various factors can affect the performance of a chemical compass from the unique perspective of quantum coherence assisted metrology. This represents a crucial step to affirm a direct connection between quantum coherence and the function of a chemical compass.
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.
Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory
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.
Clouds in Super-Earth Atmospheres: Chemical Equilibrium Calculations
Mbarek, Rostom
2016-01-01
Recent studies have unequivocally proven the existence of clouds in super-Earth atmospheres (Kreidberg et al. 2014). Here we provide a theoretical context for the formation of super-Earth clouds by determining which condensates are likely to form under the assumption of chemical equilibrium. We study super-Earth atmospheres of diverse bulk composition, which are assumed to form by outgassing from a solid core of chondritic material, following Schaefer & Fegley (2010). The super-Earth atmospheres that we study arise from planetary cores made up of individual types of chondritic meteorites. They range from highly reducing to oxidizing and have carbon to oxygen (C:O) ratios that are both subsolar and super-solar, thereby spanning a range of atmospheric composition that is appropriate for low-mass exoplanets. Given the atomic makeup of these atmospheres, we minimize the global Gibbs free energy of formation for over 550 gases and condensates to obtain the molecular composition of the atmospheres over a temper...
STANDARD CALCULATION PER PRODUCT IN THE CHEMICAL FERTILIZER INDUSTRY
Directory of Open Access Journals (Sweden)
Ion Ionescu
2016-12-01
Full Text Available The main goal of the research is to present a way of organising the managerial accounting of totally and semi finished product obtained in chemical fertilizer industry entities. For this study, we analyzed the current principle of managerial accounting to an entity in the studied area, in order to emphasize the need of organizing and implementing a modern accounting management to control the cost and increase the performance of the entities in this area, starting from the premise that there are sufficient similarities between entities in the field. Research carried out has revealed that currently, the costing is organized in terms of using traditional methods and that it is necessary to organize and implement an accounting management based on the use of modern methods, namely the method of standard costs combined with the method of centres of costs. The major implications of the proposed system for the investigated field consist of determining a relevant cost-oriented management entity, highlighting the shortcomings of traditional methods of cost
Calculations of Bose-Einstein correlations from Relativistic Quantum Molecular Dynamics
Energy Technology Data Exchange (ETDEWEB)
Sullivan, J.P.; Berenguer, M.; Fields, D.E.; Jacak, B.V.; Sarabura, M.; Simon-Gillo, J.; Sorge, H.; van Hecke, H. [Los Alamos National Lab., NM (United States); Pratt, S. [Michigan State Univ., East Lansing, MI (United States)
1993-10-01
Bose-Einstein correlation functions which are in good agreement with pion data can be calculated from an event generator. Here pion and (preliminary) kaon data from CERN experiment NA44 are compared to the calculations. The dynamics of 200 GeV/nucleon {sup 32}S + Pb collisions are calculated, without correlations due to interference patterns of a many-body wavefunction for identical particles, using the Relativistic Quantum Molecular Dynamics model (RQMD). The model is used to generate the phase-space coordinates of the emitted hadrons at the time they suffer their last strong interaction (freeze-out). Using the freeze-out position and momentum of pairs of randomly selected identical particles, a two-particle symmetrized wave-function is calculated and used to add two-body correlations. Details of the technique have been described previously. The method is similar to that used in the Spacer program.
Microwave, High-Resolution Infrared, and Quantum Chemical Investigations of CHBrF2
DEFF Research Database (Denmark)
Cazzoli, Gabriele; Cludi, Lino; Puzzarini, Cristina
2011-01-01
analysis by high-level quantum chemical calculations at the coupled-cluster level. In this context, the importance of relativistic effects, which are of the order of 6.5% and included in the present work using second-order direct perturbation theory, needs to be emphasized for accurate predictions......A combined microwave, infrared, and computational investigation of CHBrF2 is reported. For the vibrational ground state, measurements in the millimeter- and sub-millimeter-wave regions for (CHBrF2)-Br-79 and (CHBrF2)-Br-81 provided rotational and centrifugal-distortion constants up to the sextic...... terms as well as the hyperfine parameters (quadrupole-coupling and spin-rotation interaction constants) of the bromine nucleus. The determination of the latter was made possible by recording of spectra at sub-Doppler resolution, achieved by means of the Lamb-dip technique, and supporting the spectra...
Robust large-gap quantum spin Hall insulators in chemically decorated arsenene films
Wang, Dongchao; Chen, Li; Shi, Changmin; Wang, Xiaoli; Cui, Guangliang; Zhang, Pinhua; Chen, Yeqing
2016-03-01
Based on first-principles calculations, we propose one new category of two-dimensional topological insulators (2D TIs) in chemically functionalized (-CH3 and -OH) arsenene films. The results show that the surface decorated arsenene (AsCH3 and AsOH) films are intrinsic 2D TIs with sizeable bulk gap. The bulk energy gaps are 0.184 eV, and 0.304 eV in AsCH3 and AsOH films, respectively. Such large bulk gaps make them suitable to realize quantum spin Hall effect in an experimentally accessible temperature regime. Topologically helical edge states in these systems are desirable for dissipationless transport. Moreover, we find that the topological properties in these systems are robust against mechanical deformation by exerting biaxial strain. These novel 2D TIs with large bulk gaps are potential candidate in future electronic devices with ultralow dissipation.
Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han
2013-12-02
The influence of electronic and steric effects on the stabilities of carbamates formed from the reaction of CO2 with a wide range of alkanolamines was investigated by quantum chemical methods. For the calculations, B3LYP, M11-L, MP2, and spin-component-scaled MP2 (SCS-MP2) methods were used, coupled with SMD and SM8 solvation models. A reduction in carbamate stability leads to an increased CO2 absorption capacity of the amine and a reduction of the energy required for solvent regeneration. Important factors for the reduction of the carbamate stability were an increase in steric hindrance around the nitrogen atom, charge on the N atom and intramolecular hydrogen bond strength. The present study indicates that secondary ethanolamines with sterically hindering groups near the N atom show significant potential as candidates for industrial CO2-capture solvents.
Water quality index calculated from biological, physical and chemical attributes.
Rocha, Francisco Cleiton; Andrade, Eunice Maia; Lopes, Fernando Bezerra
2015-01-01
To ensure a safe drinking water supply, it is necessary to protect water quality. To classify the suitability of the Orós Reservoir (Northeast of Brazil) water for human consumption, a Water Quality Index (WQI) was enhanced and refined through a Principal Component Analysis (PCA). Samples were collected bi-monthly at seven points (P1 - P7) from July 2009 to July 2011. Samples were analysed for 29 physico-chemical attributes and 4 macroinvertebrate metrics associated with the macrophytes Pistia stratiotes and Eichhornia crassipes. PCA allowed us to reduce the number of attributes from 33 to 12, and 85.32% of the variance was explained in five dimensions (C1 - C5). Components C1 and C3 were related to water-soluble salts and reflect the weathering process, while C2 was related to surface runoff. C4 was associated with macroinvertebrate diversity, represented by ten pollution-resistant families. C5 was related to the nutrient phosphorus, an indicator of the degree of eutrophication. The mean values for the WQIs ranged from 49 to 65 (rated as fair), indicating that water can be used for human consumption after treatment. The lowest values for the WQI were recorded at the entry points to the reservoir (P3, P1, P5, and P4), while the best WQIs were recorded at the exit points (P6 and P7), highlighting the reservoir's purification ability. The proposed WQI adequately expressed water quality, and can be used for monitoring surface water quality.
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
Based on theoretical linear solvation energy relationship and quantum chemical descriptors computed by AM1 Hamiltonian, a new model is developed to predict the partitioning of some volatile organic compounds between the plant cuticular matrix and air.
SU-E-T-191: First Principle Calculation of Quantum Yield in Photodynamic Therapy
Energy Technology Data Exchange (ETDEWEB)
Abolfath, R; Guo, F; Chen, Z; Nath, R [Yale New Haven Hospital, New Haven, CT (United States)
2014-06-01
Purpose: We present a first-principle method to calculate the spin transfer efficiency in oxygen induced by any photon fields especially in MeV energy range. The optical pumping is mediated through photosensitizers, e.g., porphyrin and/or ensemble of quantum dots. Methods: Under normal conditions, oxygen molecules are in the relatively non-reactive triplet state. In the presence of certain photosensitizer compounds such as porphyrins, electromagnetic radiation of specific wavelengths can excite oxygen to highly reactive singlet state. With selective uptake of photosensitizers by certain malignant cells, photon irradiation of phosensitized tumors can lead to selective killing of cancer cells. This is the basis of photodynamic therapy (PDT). Despite several attempts, PDT has not been clinically successful except in limited superficial cancers. Many parameters such as photon energy, conjugation with quantum dots etc. can be potentially combined with PDT in order to extend the role of PDT in cancer management. The key quantity for this optimization is the spin transfer efficiency in oxygen by any photon field. The first principle calculation model presented here, is an attempt to fill this need. We employ stochastic density matrix description of the quantum jumps and the rate equation methods in quantum optics based on Markov/Poisson processes and calculate time evolution of the population of the optically pumped singlet oxygen. Results: The results demonstrate the feasibility of our model in showing the dependence of the optical yield in generating spin-singlet oxygen on the experimental conditions. The adjustable variables can be tuned to maximize the population of the singlet oxygen hence the efficacy of the photodynamic therapy. Conclusion: The present model can be employed to fit and analyze the experimental data and possibly to assist researchers in optimizing the experimental conditions in photodynamic therapy.
Quantum computing applied to calculations of molecular energies: CH2 benchmark.
Veis, Libor; Pittner, Jiří
2010-11-21
Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704 (2005)] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH(2) molecule. This molecule was chosen as a benchmark, since its two lowest lying (1)A(1) states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case.
Quantum-Mechanical Definition of Atoms and Chemical Bonds in Molecules
2015-01-01
AFRL-RQ-ED-TR-2014-0025 Quantum-Mechanical Definition of Atoms and Chemical Bonds in Molecules P.W. Langhoff J.D. Mills J.A...manufacture, use, or sell any patented invention that may relate to them. Qualified requestors may obtain copies of this report from the Defense...DATES COVERED (From - To) 15 Oct 2013 - 15 Oct 2014 4. TITLE AND SUBTITLE Quantum-Mechanical Definition of Atoms and Chemical Bonds in Molecules
Arjunan, V.; Thillai Govindaraja, S.; Jose, Sujin P.; Mohan, S.
2014-07-01
The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G**, high level 6-311++G** and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors.
Institute of Scientific and Technical Information of China (English)
FAN Hong-Yi; FAN Yue
2002-01-01
By virtue of the technique of integration within an ordered product of operators and the Schmidt decomposition of the entangled state |η〉, we reduce the general projection calculation in the theory of quantum teleportation to a as simple as possible form and present a general formalism for teleportating quantum states of continuous variable.
Kamachi, Takashi; Yoshizawa, Kazunari
2016-02-22
A conformational search program for finding low-energy conformations of large noncovalent complexes has been developed. A quantitatively reliable semiempirical quantum mechanical PM6-DH+ method, which is able to accurately describe noncovalent interactions at a low computational cost, was employed in contrast to conventional conformational search programs in which molecular mechanical methods are usually adopted. Our approach is based on the low-mode method whereby an initial structure is perturbed along one of its low-mode eigenvectors to generate new conformations. This method was applied to determine the most stable conformation of transition state for enantioselective alkylation by the Maruoka and cinchona alkaloid catalysts and Hantzsch ester hydrogenation of imines by chiral phosphoric acid. Besides successfully reproducing the previously reported most stable DFT conformations, the conformational search with the semiempirical quantum mechanical calculations newly discovered a more stable conformation at a low computational cost.
An optimized initialization algorithm to ensure accuracy in quantum Monte Carlo calculations.
Fisher, Daniel R; Kent, David R; Feldmann, Michael T; Goddard, William A
2008-11-15
Quantum Monte Carlo (QMC) calculations require the generation of random electronic configurations with respect to a desired probability density, usually the square of the magnitude of the wavefunction. In most cases, the Metropolis algorithm is used to generate a sequence of configurations in a Markov chain. This method has an inherent equilibration phase, during which the configurations are not representative of the desired density and must be discarded. If statistics are gathered before the walkers have equilibrated, contamination by nonequilibrated configurations can greatly reduce the accuracy of the results. Because separate Markov chains must be equilibrated for the walkers on each processor, the use of a long equilibration phase has a profoundly detrimental effect on the efficiency of large parallel calculations. The stratified atomic walker initialization (STRAW) shortens the equilibration phase of QMC calculations by generating statistically independent electronic configurations in regions of high probability density. This ensures the accuracy of calculations by avoiding contamination by nonequilibrated configurations. Shortening the length of the equilibration phase also results in significant improvements in the efficiency of parallel calculations, which reduces the total computational run time. For example, using STRAW rather than a standard initialization method in 512 processor calculations reduces the amount of time needed to calculate the energy expectation value of a trial function for a molecule of the energetic material RDX to within 0.01 au by 33%.
Coccia, E; Marinetti, F; Bodo, E; Gianturco, F A
2008-04-07
Diffusion Monte Carlo calculations are carried out for clusters of OH- (1Sigma+) with N 4He atoms, N varying up to 15, while classical configurations from a genetic algorithm optimization are obtained up to N=20. The overall interaction potential is assembled from ab initio data for the partners using the sum-of-potentials scheme. In contrast with the cationic dopants' behavior, the results indicate a very marked spatial delocalization and quantum features of the solvent adatoms surrounding the anionic impurity, thus making classical calculations of solvent's spatial locations of only limited use. In spite of the generally known repulsive interaction of negative charges in He droplets, the calculations show that this polar molecular anion is solvated by a liquidlike solvent layer, reminiscent of what happens in pure helium droplets.
Many-body effects on graphene conductivity: Quantum Monte Carlo calculations
Boyda, D. L.; Braguta, V. V.; Katsnelson, M. I.; Ulybyshev, M. V.
2016-08-01
Optical conductivity of graphene is studied using quantum Monte Carlo calculations. We start from a Euclidean current-current correlator and extract σ (ω ) from Green-Kubo relations using the Backus-Gilbert method. Calculations were performed both for long-range interactions and taking into account only the contact term. In both cases we vary interaction strength and study its influence on optical conductivity. We compare our results with previous theoretical calculations choosing ω ≈κ , thus working in the region of the plateau in σ (ω ) which corresponds to optical conductivity of Dirac quasiparticles. No dependence of optical conductivity on interaction strength is observed unless we approach the antiferromagnetic phase transition in the case of an artificially enhanced contact term. Our results strongly support previous theoretical studies that claimed very weak regularization of graphene conductivity.
Vusovich, O. V.; Tchaikovskaya, O. N.; Sokolova, I. V.; Vasil'eva, N. Yu.
2014-05-01
Methods of electronic spectroscopy and quantum chemistry are used to compare protolytic vanillin and isovanillin species. Three protolytic species: anion, cation, and neutral are distinguished in the ground state of the examined molecules. Vanillin and isovanillin in the ground state in water possess identical spectral characteristics: line positions and intensities in the absorption spectra coincide. Minima of the electrostatic potential demonstrate that the deepest isomer minimum is observed on the carbonyl oxygen atom. However, investigations of the fluorescence spectra show that the radiative properties of isomers differ. An analysis of results of quantum-chemical calculations demonstrate that the long-wavelength ππ* transition in the vanillin absorption spectra is formed due to electron charge transfer from the phenol part of the molecule to oxygen atoms of the methoxy and carbonyl groups, and in the isovanillin absorption spectra, it is formed only on the oxygen atom of the methoxy group. The presence of hydroxyl and carbonyl groups in the structure of the examined molecules leads to the fact that isovanillin in the ground S0 state, the same as vanillin, possesses acidic properties, whereas in the excited S1 state, they possess basic properties. A comparison of the рKа values of aqueous solutions demonstrates that vanillin possesses stronger acidic and basic properties in comparison with isovanillin.
An ab initio quantum chemical investigation of the structure and stability of ozone-water complexes
Energy Technology Data Exchange (ETDEWEB)
Kumar, Pradeep [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Sathyamurthy, N., E-mail: nsath@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli 140306 (India)
2013-03-29
Highlights: ► Eclipse geometry most stable for the 1:1 ozone-water complex. ► Cyclic structure most stable for the 1:2 complex. ► Shift in the vertical electronic excitation energy of ozone due to hydration. - Abstract: Ab initio quantum chemical calculations have been carried out to investigate the structure and stability of 1:1 and 1:2 ozone-water complexes. All the geometries have been optimized at the CCSD level of theory using aug-cc-pVDZ and aug-cc-pVTZ basis sets. The importance of correlation-consistent basis sets in deciding the nature of critical points on these complexes is emphasized. An analysis based on the dipole moment of the complexes and the charge distribution on atoms follows. The effect of ozone molecule on the structure and properties of water dimer is also investigated. Values of the vertical electronic excitation energy and the corresponding transition dipole moment have been calculated for the ozone-water complexes using the multi-reference-configuration-interaction method and the aug-cc-pVTZ basis set. The calculated shift in vibrational frequencies due to complex formation is compared with the earlier reported experimental and theoretical values.
Theoretical study of fMet-tRNA and fAla-tRNA structures by using quantum calculation
Directory of Open Access Journals (Sweden)
M. Noei
2016-11-01
Full Text Available In the prokaryotes, protein synthesis always starts with N-formylmethionine amino acid. Comparison of this amino acid with other amino acids is attempted and that is why formylmethionine is always the first amino acid to begin protein synthesis, in this paper we added a formyl group to alanine amino acid and then studied it when attached to the tRNA molecule and compared this structure with formylmethionine-tRNA structure. The quantum chemical calculations have performed using Gaussian 03 suite of programs. The fAla-tRNA and fMet-tRNA structures have fully optimized at the HF and B3LYP levels with 3–21G∗ and 6–31G∗ basis sets as well as MP2/3–21G∗ level and theoretically solvent effects on the structures were investigated. Then we studied electronic structures of the compounds using Natural Bond Orbital (NBO analysis and calculated NMR parameters at the gas-phase. Frequency analysis was also calculated at the HF and B3LYP/3-21G∗ levels in the different solvents in 298.15 K, 310.15 K temperatures and 1.00 atmosphere pressure.
Laptyeva, T. V.; Kozinov, E. A.; Meyerov, I. B.; Ivanchenko, M. V.; Denisov, S. V.; Hänggi, P.
2016-04-01
We present a numerical approach to calculate non-equilibrium eigenstates of a periodically time-modulated quantum system. The approach is based on the use of a chain of single-step propagating operators. Each operator is time-specific and constructed by combining the Magnus expansion of the time-dependent system Hamiltonian with the Chebyshev expansion of an operator exponent. The construction of the unitary Floquet operator, which evolves a system state over the full modulation period, is performed by propagating the identity matrix over the period. The independence of the evolution of basis vectors makes the propagation stage suitable for realization on a parallel cluster. Once the propagation stage is completed, a routine diagonalization of the Floquet matrix is performed. Finally, an additional propagation round, now involving the eigenvectors as the initial states, allows to resolve the time-dependence of the Floquet states and calculate their characteristics. We demonstrate the accuracy and scalability of the algorithm by applying it to calculate the Floquet states of two quantum models, namely (i) a synthesized random-matrix Hamiltonian and (ii) a many-body Bose-Hubbard dimer, both of the size up to 104 states.
A theoretical model for calculation of the detective quantum efficiency in granular scintillators
Energy Technology Data Exchange (ETDEWEB)
Cavouras, D. E-mail: cavouras@hol.gr; Kandarakis, I.; Tsoukos, S.; Kateris, A.; Nomicos, C.D.; Panayiotakis, G.S
2001-11-01
A theoretical model has been developed for calculating the detective quantum efficiency (DQE) of scintillators, by taking into account the internal structure of granular scintillators often used in medical imaging detectors. Scintillators were considered to consist of N elementary thin layers containing spherical scintillating grains of equal size. Grains were assumed to be regularly distributed within each thin layer, the thickness of the latter being equal to the grain diameter. Values of the X-ray absorption and X-ray attenuation coefficients, of the intrinsic X-ray to light conversion efficiency and of the optical scattering and absorption coefficients were used as input data to the model. Optical scattering and optical absorption coefficients were determined by fitting the model to experimental luminescence data. The model was employed to calculate the detective quantum efficiency of La{sub 2}O{sub 2}S:Tb, Y{sub 2}O{sub 2}S:Tb, Y{sub 2}O{sub 2}S:Eu, ZnSCdS:Ag, ZnSCdS:Au,Cu scintillators. Results of the calculations were found close to values published in previous studies.
Jansen, Thomas la Cour; Knoester, Jasper
2007-01-01
We combine numerical Langevin simulations with numerical integration of the Schrodinger equation to calculate two-dimensional infrared spectra of ultrafast chemical exchange. This provides a tool to model and interpret such spectra of molecules undergoing chemical processes, such as isomerization an
Calculation of Equation of State of QCD at Finite Chemical Potential and Temperature
Institute of Scientific and Technical Information of China (English)
QIAO Qing-Peng; ZONG Hong-Shi; TANG Jian; HOU Feng-Yao; LI Xue-Qian; SUN Wei-Min; L(U) Xiao-Fu
2008-01-01
In this paper, using path integral techniques we derive a model-independent formula for the pressure density (μ, T) (or equivalently the partition function) of Quantum Chromodynamics (QCD), which gives the equation of state (EOS) of QCD at finite chemical potential and temperature. In this formula the pressure density (μ, T) consists of two terms: the first term (μ,T) T=0) is a #-independent (but T-dependent) constant; the second term is totally determined by G[μ, T] (p ωn) (the dressed quark propagator at finite μ and finite T), which contains all the nontrivial μ-dependence. Then, in the framework of the rainbow-ladder approximation of the Dyson-Schwinger (DS) approach and under the approximation of neglecting the μ-dependence of the dressed gluon propagator, we show that G[μ, T] (p, ωn) can be obtained from G[T] (p, ωn) (the dressed quark propagator at μ = 0) by the substitution ωn →ωn + iμ. This result facilitates numerical calculations considerably. By this result, once G[T](p, ωn) is known, one can determine the EOS of QCD under the above approximations (up to the additive term (μ, T)[T=0). Finally, a comparison of the present EOS of QCD and the EOS obtained in the previous literatures in the framework of the rainbow-ladder approximation of the DS approach is given. It is found that the EOS given in the previous literatures does not satisfy the thermodynamic relation p(μ, T) = T.
Trail-Needs pseudopotentials in quantum Monte Carlo calculations with plane-wave/blip basis sets
Drummond, N. D.; Trail, J. R.; Needs, R. J.
2016-10-01
We report a systematic analysis of the performance of a widely used set of Dirac-Fock pseudopotentials for quantum Monte Carlo (QMC) calculations. We study each atom in the periodic table from hydrogen (Z =1 ) to mercury (Z =80 ), with the exception of the 4 f elements (57 ≤Z ≤70 ). We demonstrate that ghost states are a potentially serious problem when plane-wave basis sets are used in density functional theory (DFT) orbital-generation calculations, but that this problem can be almost entirely eliminated by choosing the s channel to be local in the DFT calculation; the d channel can then be chosen to be local in subsequent QMC calculations, which generally leads to more accurate results. We investigate the achievable energy variance per electron with different levels of trial wave function and we determine appropriate plane-wave cutoff energies for DFT calculations for each pseudopotential. We demonstrate that the so-called "T-move" scheme in diffusion Monte Carlo is essential for many elements. We investigate the optimal choice of spherical integration rule for pseudopotential projectors in QMC calculations. The information reported here will prove crucial in the planning and execution of QMC projects involving beyond-first-row elements.
Theory of Finite Size Effects for Electronic Quantum Monte Carlo Calculations of Liquids and Solids
Holzmann, Markus; Morales, Miguel A; Tubmann, Norm M; Ceperley, David M; Pierleoni, Carlo
2016-01-01
Concentrating on zero temperature Quantum Monte Carlo calculations of electronic systems, we give a general description of the theory of finite size extrapolations of energies to the thermodynamic limit based on one and two-body correlation functions. We introduce new effective procedures, such as using the potential and wavefunction split-up into long and short range functions to simplify the method and we discuss how to treat backflow wavefunctions. Then we explicitly test the accuracy of our method to correct finite size errors on example hydrogen and helium many-body systems and show that the finite size bias can be drastically reduced for even small systems.
An approximate framework for quantum transport calculation with model order reduction
Energy Technology Data Exchange (ETDEWEB)
Chen, Quan, E-mail: quanchen@eee.hku.hk [Department of Electrical and Electronic Engineering, The University of Hong Kong (Hong Kong); Li, Jun [Department of Chemistry, The University of Hong Kong (Hong Kong); Yam, Chiyung [Beijing Computational Science Research Center (China); Zhang, Yu [Department of Chemistry, The University of Hong Kong (Hong Kong); Wong, Ngai [Department of Electrical and Electronic Engineering, The University of Hong Kong (Hong Kong); Chen, Guanhua [Department of Chemistry, The University of Hong Kong (Hong Kong)
2015-04-01
A new approximate computational framework is proposed for computing the non-equilibrium charge density in the context of the non-equilibrium Green's function (NEGF) method for quantum mechanical transport problems. The framework consists of a new formulation, called the X-formulation, for single-energy density calculation based on the solution of sparse linear systems, and a projection-based nonlinear model order reduction (MOR) approach to address the large number of energy points required for large applied biases. The advantages of the new methods are confirmed by numerical experiments.
Calculation of Visible Absorption Maxima of Phthalocyanine Compounds by Quantum Theory
Institute of Scientific and Technical Information of China (English)
Shen Feng YUAN; Zhi Rong CHEN; Huai Xun CAI
2003-01-01
Based on HYPERCHEM, the structures of five phthalocyanie compounds were optimized with PM3 and their visible absorption maxima were calculated with ZINDO/S method by selecting appropriate π-π overlap weighting factor (OWFπ-π), the agreement with experiment was excellent. The relationship between OWFπ-π and molecular structure parameters was obtained by the method of stepwise regression and was explained in terms of quantum theory. OWFπ-π=0.58126+0.04562ANC1+0.03839X. Where, ANC1 and X are the symbols of average net charges on coordinated bonded nitrogens and electronegativity of central atom, respectively.
An Approximate Framework for Quantum Transport Calculation with Model Order Reduction
Chen, Quan; Yam, Chiyung; Zhang, Yu; Wong, Ngai; Chen, Guanhua
2014-01-01
A new approximate computational framework is proposed for computing the non-equilibrium charge density in the context of the non-equilibrium Green's function (NEGF) method for quantum mechanical transport problems. The framework consists of a new formulation, called the X-formulation, for single-energy density calculation based on the solution of sparse linear systems, and a projection-based nonlinear model order reduction (MOR) approach to address the large number of energy points required for large applied biases. The advantages of the new methods are confirmed by numerical experiments.
Ni, G; Ni, Guang-jiong; Wang, Haibin
1997-01-01
A simple but effective method for regularization-renormalization (R-R) is proposed for handling the Feynman diagram integral (FDI) at one loop level in quantum electrodynamics (QED). The divergence is substituted by some constants to be fixed via experiments. So no counter term, no bare parameter and no arbitrary running mass scale is involved. Then the Lamb Shift in Hydrogen atom can be calculated qualitatively and simply as $\\Delta E(2S_{1/2})- \\Delta E(2P_{1/2})=996.7 MHz$ versus the experimental value $1057.85 MHz$.
Quantum dynamics calculation of reaction probability for H+Cl2→HCl+Cl
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + Cl2 based on the GHNS potential energy surface with total angular momentum J = 0. The effects of the translational, vibrational and rotational excitation of Cl2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Quantum dynamics calculation of reaction probability for H+Cl2→HC1+Cl
Institute of Scientific and Technical Information of China (English)
王胜龙; 赵新生
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + CI2 based on the GHNS potential energy surface with total angular momentum J= 0. The effects of the translational, vibrational and rotational excitation of CI2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Institute of Scientific and Technical Information of China (English)
Ge Yu-Cheng
2008-01-01
This paper calculates quantum-mechanically the photoelectron energy spectra excited by attosecond x-rays in the presence of a few-cycle laser. A photoelectron laser phase determination method is used for precise measurements of the pulse natural properties of x-ray intensity and the instantaneous frequency profiles. As a direct procedure without any previous pulse profile assumptions and time-resolved measurements as well as data fitting analysis, this method can be used to improve the time resolutions of attosecond timing and measurements with metrological precision. The measurement range is half of a laser optical cycle.
Error sensitivity to environmental noise in quantum circuits for chemical state preparation
Sawaya, Nicolas P D; McClean, Jarrod R; Aspuru-Guzik, Alán
2016-01-01
Calculating molecular energies is likely to be one of the first useful applications to achieve quantum supremacy, performing faster on a quantum than a classical computer. However, if future quantum devices are to produce accurate calculations, errors due to environmental noise and algorithmic approximations need to be characterized and reduced. In this study, we use the high performance qHiPSTER software to investigate the effects of environmental noise on the preparation of quantum chemistry states. We simulate nineteen 16-qubit quantum circuits under environmental noise, each corresponding to a unitary coupled cluster state preparation of a different molecule or molecular configuration. Additionally, we analyze the nature of simple gate errors in noise-free circuits of up to 40 qubits. We find that the Jordan-Wigner (JW) encoding produces consistently smaller errors under a noisy environment as compared to the Bravyi-Kitaev (BK) encoding. For the JW encoding, pure-dephasing noise is shown to produce substa...
The calculation of quark number susceptibility at finite chemical potential and temperature
Energy Technology Data Exchange (ETDEWEB)
Jiang Yu; Li Ning [Department of Physics, Nanjing University, Nanjing 210093 (China); Sun Weimin [Department of Physics, Nanjing University, Nanjing 210093 (China); Joint Center for Particle, Nuclear Physics and Cosmology, Nanjing 210093 (China); Zong Hongshi, E-mail: zonghs@chenwang.nju.edu.c [Department of Physics, Nanjing University, Nanjing 210093 (China); Joint Center for Particle, Nuclear Physics and Cosmology, Nanjing 210093 (China)
2010-03-01
In this paper, we calculate the quark number susceptibility (QNS) at finite chemical potential mu and finite temperature T in the framework of the Dyson-Schwinger approach using the meromorphic quark propagator proposed in [Phys. Rev. D 70, 014014 (2004)]. Analysis and discussions of the calculated result of the QNS is given.
The complete quantum collapse scenario of 2+1 dust shell: Preliminary Calculations
Ortiz, L
2007-01-01
If we consider the gravitational collapse of a material object to a black hole, we would expect, for ranges of mass where a black hole would form, the following scenario. A large enough object would collapse classically until an event horizon forms, and to an external observer the object would be lost fom view. However, once the horizon has formed the black hole will begin to emit Hawking radiation and the hole will lose mass and the horizon will shrink. The final state of this process could be either a zero-mass "black hole" with consequent information loss, or some sort of "quantum remnant. A complete investigation of this process would require: 1) A complete and consistent theory of quantum gravity coupled to some kind of field that would provide the Hawking radiation (which could be the gravitational field itself --gravitons); 2) Some kind of definition of a "horizon" in this quantum gravity, and; 3) The calculational tools to achieve a description of the scenario. Lacking these, one may resort to toy mod...
Chemical Exchange Saturation Transfer (CEST) Agents: Quantum Chemistry and MRI.
Li, Jikun; Feng, Xinxin; Zhu, Wei; Oskolkov, Nikita; Zhou, Tianhui; Kim, Boo Kyung; Baig, Noman; McMahon, Michael T; Oldfield, Eric
2016-01-04
Diamagnetic chemical exchange saturation transfer (CEST) contrast agents offer an alternative to Gd(3+) -based contrast agents for MRI. They are characterized by containing protons that can rapidly exchange with water and it is advantageous to have these protons resonate in a spectral window that is far removed from water. Herein, we report the first results of DFT calculations of the (1) H nuclear magnetic shieldings in 41 CEST agents, finding that the experimental shifts can be well predicted (R(2) =0.882). We tested a subset of compounds with the best MRI properties for toxicity and for activity as uncouplers, then obtained mice kidney CEST MRI images for three of the most promising leads finding 16 (2,4-dihydroxybenzoic acid) to be one of the most promising CEST MRI contrast agents to date. Overall, the results are of interest since they show that (1) H NMR shifts for CEST agents-charged species-can be well predicted, and that several leads have low toxicity and yield good in vivo MR images.
Quantum limit for avian magnetoreception: How sensitive can a chemical compass be?
Cai, Jianming; Plenio, Martin B
2011-01-01
The chemical compass model, based on radical pair reactions, is a fascinating idea to explain avian magnetoreception. At present, questions concerning the key ingredients responsible for the high sensitivity of a chemical compass and the possible role of quantum coherence and decoherence remain unsolved. Here, we investigate the optimized hyperfine coupling for a chemical compass in order to achieve the best magnetic field sensitivity. We demonstrate that its magnetic sensitivity limit can be further extended by simple quantum control and may benefit from additional decoherence. The present results also provide routes towards the design a biomimetic weak magnetic field sensor.
Directory of Open Access Journals (Sweden)
Zhengde Tan
2013-01-01
Full Text Available In comparison with the Q-e scheme, the Revised Patterns Scheme: the U, V Version (the U-V scheme has greatly improved both its accessibility and its accuracy in interpreting and predicting the reactivity of a monomer in free-radical copolymerizations. Quantitative structure-activity relationship (QSAR models were developed to predict the reactivity parameters u and v of the U-V scheme, by applying genetic algorithm (GA and support vector machine (SVM techniques. Quantum chemical descriptors used for QSAR models were calculated from transition state species with structures C¹H3 - C²HR³• or •C¹H2 - C²H2R³ (formed from vinyl monomers C¹H²=C²HR³ + H•, using density functional theory (DFT, at the UB3LYP level of theory with 6-31G(d basis set. The optimum support vector regression (SVR model of the reactivity parameter u based on Gaussian radial basis function (RBF kernel (C = 10, ε = 10- 5 and γ = 1.0 produced root-mean-square (rms errors for the training, validation and prediction sets being 0.220, 0.326 and 0.345, respectively. The optimal SVR model for v with the RBF kernel (C = 20, ε = 10- 4 and γ = 1.2 produced rms errors for the training set of 0.123, the validation set of 0.206 and the prediction set of 0.238. The feasibility of applying the transition state quantum chemical descriptors to develop SVM models for reactivity parameters u and v in the U-V scheme has been demonstrated.
Proton exchange between oxymethyl radical and acids and bases: semiempirical quantum-chemical study
Directory of Open Access Journals (Sweden)
Irina Pustolaikina
2016-12-01
Full Text Available The reactions with proton participation are widely represented in the analytical, technological and biological chemistry. Quantum-chemical study of the exchange processes in hydrogen bonding complexes will allow us to achieve progress in the understanding of the elementary act mechanism of proton transfer in hydrogen bonding chain as well as the essence of the acid-base interactions. Oxymethyl radical •CH2ОН is small in size and comfortable as a model particle that well transmits protolytic properties of paramagnetic acids having more complex structure. Quantum-chemical modeling of proton exchange reaction oxymethyl radical ∙CH2OH and its diamagnetic analog CH3OH with amines, carboxylic acids and water was carried out using UAM1 method with the help of Gaussian-2009 program. QST2 method was used for the search of transition state, IRC procedure was applied for the calculation of descents along the reaction coordinate. The difference in the structure of transition states of ∙CH2OH/ CH3OH with bases and acids has been shown. It has been confirmed that in the case of bases, consecutive proton exchange mechanism was fixed, and in the case of complexes with carboxylic acids parallel proton exchange mechanism was fixed. The similarity in the reaction behavior of paramagnetic and diamagnetic systems in the proton exchange has been found. It was suggested that the mechanism of proton exchange reaction is determined by the structure of the hydrogen bonding cyclic complex, which is, in turn, depends from the nature of the acid-base interactions partners.
Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics
DEFF Research Database (Denmark)
Bratholm, Lars Andersen
to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....... experimental data in the form of chemical shifts, as well as distance restraints obtained either experimentally or from sequence co-evolution. Of notable results, One of the determined structures, aKMT, was not solved experimentally at the time, but was found to match the recently published X-ray structure...
Calculation of the axion mass based on high-temperature lattice quantum chromodynamics
Borsanyi, S.; Fodor, Z.; Guenther, J.; Kampert, K.-H.; Katz, S. D.; Kawanai, T.; Kovacs, T. G.; Mages, S. W.; Pasztor, A.; Pittler, F.; Redondo, J.; Ringwald, A.; Szabo, K. K.
2016-11-01
Unlike the electroweak sector of the standard model of particle physics, quantum chromodynamics (QCD) is surprisingly symmetric under time reversal. As there is no obvious reason for QCD being so symmetric, this phenomenon poses a theoretical problem, often referred to as the strong CP problem. The most attractive solution for this requires the existence of a new particle, the axion—a promising dark-matter candidate. Here we determine the axion mass using lattice QCD, assuming that these particles are the dominant component of dark matter. The key quantities of the calculation are the equation of state of the Universe and the temperature dependence of the topological susceptibility of QCD, a quantity that is notoriously difficult to calculate, especially in the most relevant high-temperature region (up to several gigaelectronvolts). But by splitting the vacuum into different sectors and re-defining the fermionic determinants, its controlled calculation becomes feasible. Thus, our twofold prediction helps most cosmological calculations to describe the evolution of the early Universe by using the equation of state, and may be decisive for guiding experiments looking for dark-matter axions. In the next couple of years, it should be possible to confirm or rule out post-inflation axions experimentally, depending on whether the axion mass is found to be as predicted here. Alternatively, in a pre-inflation scenario, our calculation determines the universal axionic angle that corresponds to the initial condition of our Universe.
A new method to calculate Berry phase in one-dimensional quantum anomalous Hall insulator
Liao, Yi
2016-08-01
Based on the residue theorem and degenerate perturbation theory, we derive a new, simple and general formula for Berry phase calculation in a two-level system for which the Hamiltonian is a real symmetric matrix. The special torus topology possessed by the first Brillouin zone (1 BZ) of this kind of systems ensures the existence of a nonzero Berry phase. We verify the correctness of our formula on the Su-Schrieffer-Heeger (SSH) model. Then the Berry phase of one-dimensional quantum anomalous Hall insulator (1DQAHI) is calculated analytically by applying our method, the result being -π/2 -π/4 sgn (B) [ sgn (Δ - 4 B) + sgn (Δ) ]. Finally, illuminated by this idea, we investigate the Chern number in the two-dimensional case, and find a very simple way to determine the parameter range of the non-trivial Chern number in the phase diagram.
Parallelizing the QUDA Library for Multi-GPU Calculations in Lattice Quantum Chromodynamics
Energy Technology Data Exchange (ETDEWEB)
Ronald Babich, Michael Clark, Balint Joo
2010-11-01
Graphics Processing Units (GPUs) are having a transformational effect on numerical lattice quantum chromodynamics (LQCD) calculations of importance in nuclear and particle physics. The QUDA library provides a package of mixed precision sparse matrix linear solvers for LQCD applications, supporting single GPUs based on NVIDIA's Compute Unified Device Architecture (CUDA). This library, interfaced to the QDP++/Chroma framework for LQCD calculations, is currently in production use on the "9g" cluster at the Jefferson Laboratory, enabling unprecedented price/performance for a range of problems in LQCD. Nevertheless, memory constraints on current GPU devices limit the problem sizes that can be tackled. In this contribution we describe the parallelization of the QUDA library onto multiple GPUs using MPI, including strategies for the overlapping of communication and computation. We report on both weak and strong scaling for up to 32 GPUs interconnected by InfiniBand, on which we sustain in excess of 4 Tflops.
Open Quantum Dynamics Calculations with the Hierarchy Equations of Motion on Parallel Computers.
Strümpfer, Johan; Schulten, Klaus
2012-08-14
Calculating the evolution of an open quantum system, i.e., a system in contact with a thermal environment, has presented a theoretical and computational challenge for many years. With the advent of supercomputers containing large amounts of memory and many processors, the computational challenge posed by the previously intractable theoretical models can now be addressed. The hierarchy equations of motion present one such model and offer a powerful method that remained under-utilized so far due to its considerable computational expense. By exploiting concurrent processing on parallel computers the hierarchy equations of motion can be applied to biological-scale systems. Herein we introduce the quantum dynamics software PHI, that solves the hierarchical equations of motion. We describe the integrator employed by PHI and demonstrate PHI's scaling and efficiency running on large parallel computers by applying the software to the calculation of inter-complex excitation transfer between the light harvesting complexes 1 and 2 of purple photosynthetic bacteria, a 50 pigment system.
Jacob, D; Palacios, J J
2011-01-28
We study the performance of two different electrode models in quantum transport calculations based on density functional theory: parametrized Bethe lattices and quasi-one-dimensional wires or nanowires. A detailed account of implementation details in both the cases is given. From the systematic study of nanocontacts made of representative metallic elements, we can conclude that the parametrized electrode models represent an excellent compromise between computational cost and electronic structure definition as long as the aim is to compare with experiments where the precise atomic structure of the electrodes is not relevant or defined with precision. The results obtained using parametrized Bethe lattices are essentially similar to the ones obtained with quasi-one-dimensional electrodes for large enough cross-sections of these, adding a natural smearing to the transmission curves that mimics the true nature of polycrystalline electrodes. The latter are more demanding from the computational point of view, but present the advantage of expanding the range of applicability of transport calculations to situations where the electrodes have a well-defined atomic structure, as is the case for carbon nanotubes, graphene nanoribbons, or semiconducting nanowires. All the analysis is done with the help of codes developed by the authors which can be found in the quantum transport toolbox ALACANT and are publicly available.
Arjunan, V.; Marchewka, Mariusz K.; Kalaivani, M.
2012-10-01
The molecular complex of betaine with selenious acid namely, betaine dihydrogen selenite (C5H13NO5Se, BDHSe) was synthesised by the reaction of betaine and SeO2 in a 1:1:1 solution of isopropanol, methanol and water. Crystals were grown from this solution by cooling to 253 K for few days. The complex was formed without accompanying proton transfer from selenious acid molecule to betaine. The complete vibrational assignments and analysis of BDHSe have been performed by FTIR, FT-Raman and far-infrared spectral studies. More support on the experimental findings was added from the quantum chemical studies performed with DFT (B3LYP) method using 6-311++G∗∗, 6-31G∗∗, cc-pVDZ and 3-21G basis sets. The structural parameters, energies, thermodynamic parameters and the NBO charges of BDHSe were determined by the DFT method. The 1H and 13C isotropic chemical shifts (δ ppm) of BDHSe with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. SHG experiment was carried out using Kurtz-Perry powder technique. The efficiency of second harmonic generation for BDHSe was estimated relatively to KDP: deff = 0.97 deff (KDP).
Arjunan, V; Marchewka, Mariusz K; Kalaivani, M
2012-10-01
The molecular complex of betaine with selenious acid namely, betaine dihydrogen selenite (C(5)H(13)NO(5)Se, BDHSe) was synthesised by the reaction of betaine and SeO(2) in a 1:1:1 solution of isopropanol, methanol and water. Crystals were grown from this solution by cooling to 253 K for few days. The complex was formed without accompanying proton transfer from selenious acid molecule to betaine. The complete vibrational assignments and analysis of BDHSe have been performed by FTIR, FT-Raman and far-infrared spectral studies. More support on the experimental findings was added from the quantum chemical studies performed with DFT (B3LYP) method using 6-311++G(**), 6-31G(**), cc-pVDZ and 3-21G basis sets. The structural parameters, energies, thermodynamic parameters and the NBO charges of BDHSe were determined by the DFT method. The (1)H and (13)C isotropic chemical shifts (δ ppm) of BDHSe with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. SHG experiment was carried out using Kurtz-Perry powder technique. The efficiency of second harmonic generation for BDHSe was estimated relatively to KDP: d(eff)=0.97 d(eff) (KDP).
Ishikawa, Atsushi; Nakai, Hiromi
2015-03-01
The harmonic solvation model (HSM), which was recently developed for evaluating condensed-phase thermodynamics by quantum chemical calculations (Nakai and Ishikawa, 2014), was applied to formation and combustion reactions of simple organic molecules. The conventional ideal gas model (IGM) considerably overestimated the entropies of the liquid molecules. The HSM could significantly improve this overestimation; mean absolute deviations for the Gibbs energies of the formation and combustion reactions were (49.6, 26.7) for the IGM and (9.7, 5.4) for the HSM in kJ/mol.
Goker, Ali
2011-06-01
A combination of ab initio and many-body calculations is utilized to determine the effects of the bonding in Au electrodes on the time dependent current through a quantum dot suddenly shifted into the Kondo regime by a gate voltage. For an asymmetrically coupled system the instantaneous conductance exhibits fluctuations. The frequencies of the fluctuations turn out to be proportional to the energetic separation between the dominating peaks in the density of states and the Fermi level. The chemical bonding in the electrodes, thus, drastically alters the transient current, which can be accessed by ultrafast pump-probe techniques. © 2011 Elsevier B.V. All rights reserved.
Mass spectrometric and quantum chemical determination of proton water clustering equilibria
Likholyot, Alexander; Lemke, Kono H.; Hovey, Jamey K.; Seward, Terry M.
2007-05-01
We report on the thermochemistry of proton hydration by water in the gas phase both experimentally using high-pressure mass spectrometry (HPMS) and theoretically using multilevel G3, G3B3, CBS-Q, CBS-QB3, CBS/QCI-APNO as well as density functional theory (DFT) calculations. Gas phase hydration enthalpies and entropies for protonated water cluster equilibria with up to 7 waters (i.e., n ⩽ 7H 3O +·(H 2O) n) were observed and exhibited non-monotonic behavior for successive hydration steps as well as enthalpy and entropy anomalies at higher cluster rank numbers. In particular, there is a significant jump in the stepwise enthalpies and entropies of cluster formation for n varying from 6 to 8. This behavior can be successfully interpreted using cluster geometries obtained from quantum chemical calculations by considering the number of additional hydrogen bonds formed at each hydration step and simultaneous weakening of ion-solvent interaction with increasing cluster size. The measured total hydration energy for the attachment of the first six water molecules around the hydronium ion was found to account for more than 60% of total bulk hydration free energy.
Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya
2015-01-14
Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines.
Wormit, Michael; Dreuw, Andreas
2007-06-21
Light harvesting complexes (LHCs) have been identified in all photosynthetic organisms. To understand their function in light harvesting and energy dissipation, detailed knowledge about possible excitation energy transfer (EET) and electron transfer (ET) processes in these pigment proteins is of prime importance. This again requires the study of electronically excited states of the involved pigment molecules, in LHCs of chlorophylls and carotenoids. This paper represents a critical review of recent quantum chemical calculations on EET and ET processes between pigment pairs relevant for the major LHCs of green plants (LHC-II) and of purple bacteria (LH2). The theoretical methodology for a meaningful investigation of such processes is described in detail, and benefits and limitations of standard methods are discussed. The current status of excited state calculations on chlorophylls and carotenoids is outlined. It is focused on the possibility of EET and ET in the context of chlorophyll fluorescence quenching in LHC-II and carotenoid radical cation formation in LH2. In the context of non-photochemical quenching of green plants, it is shown that replacement of the carotenoid violaxanthin by zeaxanthin in its binding pocket of LHC-II can not result in efficient quenching. In LH2, our computational results give strong evidence that the S(1) states of the carotenoids are involved in carotenoid cation formation. By comparison of theoretical findings with recent experimental data, a general mechanism for carotenoid radical cation formation is suggested.
Kovács, Attila
2017-03-17
Actinide trioxide (AnO3, An = U, Np, Pu, Am, Cm) molecules have been investigated by relativistic multireference quantum chemical calculations with the goal to elucidate their electronic structures. The molecular geometries of the ground and selected excited electronic states have been optimized at the spin-orbit-free complete active space second-order perturbation theory (SF-CASPT2) level. The low-lying vertical excitation states have been computed and characterized by CASPT2 calculations taking into account spin-orbit coupling. The reason for the considerable lengthening of the equatorial An-O bond in AmO3 and CmO3 with respect to the other trioxides has been analyzed on the basis of valence molecular orbitals of the SF ground electronic states. For the bond in question a singly occupied π orbital has been identified, this orbital is doubly occupied in the other (An = U, Np, Pu) trioxides. The clarified electronic structures of the investigated AnO3 molecules confirmed the pentavalent character of Am and Cm in their trioxides in contrast to the hexavalent character of U, Np, and Pu.
Grant, Daniel J; Stewart, Timothy J; Bau, Robert; Miller, Kevin A; Mason, Sax A; Gutmann, Matthias; McIntyre, Garry J; Gagliardi, Laura; Evans, William J
2012-03-19
The unusual uranium reaction system in which uranium(4+) and uranium(3+) hydrides interconvert by formal bimetallic reductive elimination and oxidative addition reactions, [(C(5)Me(5))(2)UH(2)](2) (1) ⇌ [(C(5)Me(5))(2)UH](2) (2) + H(2), was studied by employing multiconfigurational quantum chemical and density functional theory methods. 1 can act as a formal four-electron reductant, releasing H(2) gas as the byproduct of four H(2)/H(-) redox couples. The calculated structures for both reactants and products are in good agreement with the X-ray diffraction data on 2 and 1 and the neutron diffraction data on 1 obtained under H(2) pressure as part of this study. The interconversion of the uranium(4+) and uranium(3+) hydride species was calculated to be near thermoneutral (~-2 kcal/mol). Comparison with the unknown thorium analogue, [(C(5)Me(5))(2)ThH](2), shows that the thorium(4+) to thorium(3+) hydride interconversion reaction is endothermic by 26 kcal/mol.
Keith, John A; Carter, Emily A
2012-09-11
Sensibly modeling (photo)electrocatalytic reactions involving proton and electron transfer with computational quantum chemistry requires accurate descriptions of protonated, deprotonated, and radical species in solution. Procedures to do this are generally nontrivial, especially in cases that involve radical anions that are unstable in the gas phase. Recently, pyridinium and the corresponding reduced neutral radical have been postulated as key catalysts in the reduction of CO2 to methanol. To assess practical methodologies to describe the acid/base chemistry of these species, we employed density functional theory (DFT) in tandem with implicit solvation models to calculate acidity constants for 22 substituted pyridinium cations and their corresponding pyridinyl radicals in water solvent. We first benchmarked our calculations against experimental pyridinium deprotonation energies in both gas and aqueous phases. DFT with hybrid exchange-correlation functionals provide chemical accuracy for gas-phase data and allow absolute prediction of experimental pKas with unsigned errors under 1 pKa unit. The accuracy of this economical pKa calculation approach was further verified by benchmarking against highly accurate (but very expensive) CCSD(T)-F12 calculations. We compare the relative importance and sensitivity of these energies to selection of solvation model, solvation energy definitions, implicit solvation cavity definition, basis sets, electron densities, model geometries, and mixed implicit/explicit models. After determining the most accurate model to reproduce experimentally-known pKas from first principles, we apply the same approach to predict pKas for radical pyridinyl species that have been proposed relevant under electrochemical conditions. This work provides considerable insight into the pitfalls using continuum solvation models, particularly when used for radical species.
Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye
2016-02-09
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D.
Svehla, R. A.; Mcbride, B. J.
1973-01-01
A FORTRAN IV computer program for the calculation of the thermodynamic and transport properties of complex mixtures is described. The program has the capability of performing calculations such as:(1) chemical equilibrium for assigned thermodynamic states, (2) theoretical rocket performance for both equilibrium and frozen compositions during expansion, (3) incident and reflected shock properties, and (4) Chapman-Jouguet detonation properties. Condensed species, as well as gaseous species, are considered in the thermodynamic calculation; but only the gaseous species are considered in the transport calculations.
DEFF Research Database (Denmark)
Steinmann, Casper; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob
2014-01-01
We present NMR shielding constants obtained through quantum mechanical/molecular mechanical (QM/MM) embedding calculations. Contrary to previous reports, we show that a relatively small QM region is sufficient, provided that a high-quality embedding potential is used. The calculated averaged NMR...
Analytical calculation of the quantum 1/f coherence parameter for HFETs
Handel, Peter H.; Sherif, Taher S.
2010-03-01
The ratio s of the coherent magnetic energy term and the incoherent mechanical kinetic energy terms of the drift motion in the hamiltonian of a current carrying system is calculated for the special cases of a HFET or FET. This ratio defines the resulting quantum 1/f noise from the coherent and conventional quantum 1/f effects. In this case of FETs and HFETs of much larger width w>>LDS>t, the kinetic energy Ek of average motion with drift velocity vd per unit length in the direction of the drain-source distance LDS in the channel of thickness t, is still given by Nmvd 2/2, but the magnetic energy Em per unit length in the direction of LDS is roughly proportional with the first power of w only, instead of w2, and can be approximated by Em = π[ln(w/2LDS)]LDS[nevS/c]2/w. Here S=wt is the cross section though which current flows this indicates field-decoherence along the large device width w. This yields a coherence ratio of s ≡ Em/Ek ~ πnrotLDSln(w/2LDS), which shows that only an effective width w=weff about equal to LDS should be used in the calculation of s in this special case; larger widths are subject to de-coherence. This favors lower, mainly conventional, quantum 1/f noise in these devices, in spite of the large values of w. It also explains for the first time why the huge widths are possible with impunity, i.e., without causing the much larger coherent quantum 1/f noise to appear. For non-uniform current distribution across t, and for piezoelectric coupling, improved forms are derived for s. Specifically, the coherence parameter, called s' for the piezo case, is given by s' = (gN'h/m*vs)( vs/u)3F(u/vs)t/12w, where F(u/vs) = (2/3)(u/vs) for small drift velocity u, much smaller than the sound velocity vs in the semiconductor. Here N'=nwt.
Fröhlich, Daniel R; Kremleva, Alena; Rossberg, André; Skerencak-Frech, Andrej; Koke, Carsten; Krüger, Sven; Rösch, Notker; Panak, Petra J
2017-06-19
The complexation of Am(III) with formate in aqueous solution is studied as a function of the pH value using a combination of extended X-ray absorption fine structure (EXAFS) spectroscopy, iterative transformation factor analysis (ITFA), and quantum chemical calculations. The Am LIII-edge EXAFS spectra are analyzed to determine the molecular structure (coordination numbers; Am-O and Am-C distances) of the formed Am(III)-formate species and to track the shift of the Am(III) speciation with increasing pH. The experimental data are compared to predictions from density functional calculations. The results indicate that formate binds to Am(III) in a monodentate fashion, in agreement with crystal structures of lanthanide formates. Furthermore, the investigations are complemented by thermodynamic speciation calculations to verify further the results obtained.
Kadatskiy, M. A.; Khishchenko, K. V.
2016-11-01
Quantum-statistical calculations of shock compressibility of iron are performed. Electronic part of thermodynamic functions is calculated in the framework of three quantum-statistical approaches: the Thomas-Fermi, the Thomas-Fermi with quantum and exchange corrections and the Hartree-Fock-Slater models. The influence of ionic part of thermodynamic functions is taken into account separately with using three models: the ideal gas, the one-component plasma and the charged hard spheres models. The results of calculations are presented in the pressure range from 1 to 107 GPa for samples with initially densities 7.85, 4.31 and 2.27 g/cm3. Calculated Hugoniots are compared with available experimental data.
Directory of Open Access Journals (Sweden)
B. Maiti
2002-04-01
Full Text Available Abstract: Dynamical behavior of chemical reactivity indices like electronegativity, hardness, polarizability, electrophilicity and nucleophilicity indices is studied within a quantum fluid density functional framework for the interactions of a hydrogen atom in its ground electronic state (n = 1 and an excited electronic state (n = 20 with monochromatic and bichromatic laser pulses. Time dependent analogues of various electronic structure principles like the principles of electronegativity equalization, maximum hardness, minimum polarizability and maximum entropy have been found to be operative. Insights into the variation of intensities of the generated higher order harmonics on the color of the external laser field are obtained. The quantum signature of chaos in hydrogen atom has been studied using a quantum theory of motion and quantum fluid dynamics. A hydrogen atom in the electronic ground state (n = 1 and in an excited electronic state ( n = 20 behaves differently when placed in external oscillating monochromatic and bichromatic electric fields. Temporal evolutions of Shannon entropy, quantum Lyapunov exponent and Kolmogorov Ã¢Â€Â“ Sinai entropy defined in terms of the distance between two initially close Bohmian trajectories for these two cases show marked differences. It appears that a larger uncertainty product and a smaller hardness value signal a chaotic behavior.
Directory of Open Access Journals (Sweden)
Altaf Hussain Pandith
2010-01-01
Full Text Available Quantum chemical parameters such as LUMO energy, HOMO energy, ionization energy (I, electron affinity (A, chemical potential (μ, hardness (η electronegativity (χ, philicity (ωα, and electrophilicity (ω of a series of aliphatic compounds are calculated at the B3LYP/6-31G(d level of theory. Quantitative structure-activity relationship (QSAR models are developed for predicting the toxicity (pIGC50 of 13 classes of aliphatic compounds, including 171 electron acceptors and 81 electron donors, towards Tetrahymena pyriformis. The multiple linear regression modeling of toxicity of these compounds is performed by using the molecular descriptor log P (1-octanol/water partition coefficient in conjunction with two other quantum chemical descriptors, electrophilicity (ω and energy of the lowest unoccupied molecular orbital (ELUMO. A comparison is made towards the toxicity predicting the ability of electrophilicity (ω versus ELUMO as a global chemical reactivity descriptor in addition to log P. The former works marginally better in most cases. There is a slight improvement in the quality of regression by changing the unit of IGC50 from mg/L to molarity and by removing the racemates and the diastereoisomers from the data set.
Godina-Nava, Juan José; Torres-Vega, Gabino; López-Riquelme, Germán Octavio; López-Sandoval, Eduardo; Samana, Arturo Rodolfo; García Velasco, Fermín; Hernández-Aguilar, Claudia; Domínguez-Pacheco, Arturo
2017-02-01
Using the conventional Haberkorn approach, it is evaluated the recombination of the radical pair (RP) singlet spin state to study theoretically the cytoprotective effect of an extremely-low-frequency electromagnetic field (ELF-EMF) on early stages of hepatic cancer chemically induced in rats. The proposal is that ELF-EMF modulates the interconversion rate of singlet and triplet spin states of the RP populations modifying the products from the metabolization of carcinogens. Previously, we found that the daily treatment with ELF-EMF 120 Hz inhibited the number and area of preneoplastic lesions in chemical carcinogenesis. The singlet spin population is evaluated diagonalizing the spin density matrix through the Lanczos method in a radical pair mechanism (RPM). Using four values of the interchange energy, we have studied the variations over the singlet population. The low magnetic field effect as a test of the influence over the enzymatic chemical reaction is evaluated calculating the quantum yield. Through a bootstrap technique the range is found for the singlet decay rate for the process. Applying the quantum measurements concept, we addressed the impact toward hepatic cells. The result contributes to improving our understanding of the chemical carcinogenesis process affected by charged particles that damage the DNA.
Santillana, Mauricio; Le Sager, Philippe; Jacob, Daniel J.; Brenner, Michael P.
2010-11-01
We present a computationally efficient adaptive method for calculating the time evolution of the concentrations of chemical species in global 3-D models of atmospheric chemistry. Our strategy consists of partitioning the computational domain into fast and slow regions for each chemical species at every time step. In each grid box, we group the fast species and solve for their concentration in a coupled fashion. Concentrations of the slow species are calculated using a simple semi-implicit formula. Separation of species between fast and slow is done on the fly based on their local production and loss rates. This allows for example to exclude short-lived volatile organic compounds (VOCs) and their oxidation products from chemical calculations in the remote troposphere where their concentrations are negligible, letting the simulation determine the exclusion domain and allowing species to drop out individually from the coupled chemical calculation as their production/loss rates decline. We applied our method to a 1-year simulation of global tropospheric ozone-NO x-VOC-aerosol chemistry using the GEOS-Chem model. Results show a 50% improvement in computational performance for the chemical solver, with no significant added error.
Baran, Richard; Northen, Trent R
2013-10-15
Untargeted metabolite profiling using liquid chromatography and mass spectrometry coupled via electrospray ionization is a powerful tool for the discovery of novel natural products, metabolic capabilities, and biomarkers. However, the elucidation of the identities of uncharacterized metabolites from spectral features remains challenging. A critical step in the metabolite identification workflow is the assignment of redundant spectral features (adducts, fragments, multimers) and calculation of the underlying chemical formula. Inspection of the data by experts using computational tools solving partial problems (e.g., chemical formula calculation for individual ions) can be performed to disambiguate alternative solutions and provide reliable results. However, manual curation is tedious and not readily scalable or standardized. Here we describe an automated procedure for the robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming optimization (RAMSI). Chemical rules among related ions are expressed as linear constraints and both the spectra interpretation and chemical formula calculation are performed in a single optimization step. This approach is unbiased in that it does not require predefined sets of neutral losses and positive and negative polarity spectra can be combined in a single optimization. The procedure was evaluated with 30 experimental mass spectra and was found to effectively identify the protonated or deprotonated molecule ([M + H](+) or [M - H](-)) while being robust to the presence of background ions. RAMSI provides a much-needed standardized tool for interpreting ions for subsequent identification in untargeted metabolomics workflows.
First-principles calculation of core-level binding energy shift in surface chemical processes
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.
Dattani, Nikesh S
2012-01-01
This MATLAB program calculates the dynamics of the reduced density matrix of an open quantum system modeled by the Feynman-Vernon model. The user gives the program a vector describing the coordinate of an open quantum system, a hamiltonian matrix describing its energy, and a spectral distribution function and temperature describing the environment's influence on it, in addition to the open quantum system's intial density matrix and a grid of times. With this, the program returns the reduced density matrix of the open quantum system at all (or some) moments specified by that grid of times. This overall calculation can be divided into two stages: the setup of the Feynman integral, and the actual calculation of the Feynman integral for time-propagation of the density matrix. When this program calculates this propagation on a multi-core CPU, it is this propagation that is usually the rate limiting step of the calculation, but when it is calculated on a GPU, the propagation is calculated so quickly that the setup ...
Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics
DEFF Research Database (Denmark)
Bratholm, Lars Andersen
In this thesis, my work involving dierent aspects of protein structure determination by computer modeling is presented. Determination of several protein's native fold were carried out with Markov chain Monte Carlo simulations in the PHAISTOS protein structure simulation framework, utilizing...... to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...
Mullin, Jonathan; Valley, Nicholas; Blaber, Martin G; Schatz, George C
2012-09-27
Multiscale models that combine quantum mechanics and classical electrodynamics are presented, which allow for the evaluation of surface-enhanced Raman (SERS) and hyper-Raman scattering spectra (SEHRS) for both chemical (CHEM) and electrodynamic (EM) enhancement mechanisms. In these models, time-dependent density functional theory (TDDFT) for a system consisting of the adsorbed molecule and a metal cluster fragment of the metal particle is coupled to Mie theory for the metal particle, with the surface of the cluster being overlaid with the surface of the metal particle. In model A, the electromagnetic enhancement from plasmon-excitation of the metal particle is combined with the chemical enhancement associated with a static treatment of the molecule-metal structure to determine overall spectra. In model B, the frequency dependence of the Raman spectrum of the isolated molecule is combined with the enhancements determined in model A to refine the enhancement estimate. An equivalent theory at the level of model A is developed for hyper-Raman spectra calculations. Application to pyridine interacting with a 20 nm diameter silver sphere is presented, including comparisons with an earlier model (denoted G), which combines plasmon enhanced fields with gas-phase Raman (or hyper-Raman) spectra. The EM enhancement factor for spherical particles at 357 nm is found to be 10(4) and 10(6) for SERS and SEHRS, respectively. Including both chemical and electromagnetic mechanisms at the level of model A leads to enhancements on the order of 10(4) and 10(9) for SERS and SEHRS.
Wet chemical synthesis of quantum dots for medical applications
Cepeda-Pérez, E. I.; López-Luke, T.; Pérez-Mayen, L.; Hidalgo, Alberto; de la Rosa, E.; Torres-Castro, Alejandro; Ceja-Fdez, Andrea; Vivero-Escoto, Juan; Gonzalez-Yebra, Ana L.
2015-07-01
In recent years the use of nanoparticles in medical applications has boomed. This is because the various applications that provide these materials like drug delivery, cancer cell diagnostics and therapeutics [1-5]. Biomedical applications of Quantum Dots (QDs) are focused on molecular imaging and biological sensing due to its optical properties. The size of QDs can be continuously tuned from 2 to 10 nm in diameter, which, after polymer encapsulation, generally increases to 5 - 20 nm diminishing the toxicity. The QDs prepared in our lab have a diameter between 2 to 7 nm. Particles smaller than 5 nm can interact with the cells [2]. Some of the characteristics that distinguish QDs from the commonly used fluorophores are wider range of emission, narrow and more sharply defined emission peak, brighter emission and a higher signal to noise ratio compared with organic dyes [6]. In this paper we will show our progress in the study of the interaction of quantum dots in live cells for image and Raman spectroscopy applications. We will also show the results of the interaction of quantum dots with genomic DNA for diagnostic purposes.
Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides
Sharma, Vinit; Krogel, Jaron T.; Kent, P. R. C.; Reboredo, Fernando A.
One of the critical scientific challenges of contemporary research is to obtain an accurate theoretical description of the electronic properties of strongly correlated systems such as transition metal oxides and rare-earth compounds, since state-of-art ab-initio methods based on approximate density functionals are not always sufficiently accurate. Quantum Monte Carlo (QMC) methods, which use statistical sampling to evaluate many-body wave functions, have the potential to answer this challenge. Owing to the few fundamental approximations made and the direct treatment of electron correlation, QMC methods are among the most accurate electronic structure methods available to date. We assess the accuracy of the diffusion Monte Carlo method in the case of rocksalt manganese oxide (MnO). We study the electronic properties of this strongly-correlated oxide, which has been identified as a suitable candidate for many applications ranging from catalysts to electronic devices. ``This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.'' Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides.
Kim, Sejoong; Lee, Hyun-Woo
2006-05-01
A pioneering experiment [E. Schuster, E. Buks, M. Heiblum, D. Mahalu, V. Umansky, and Hadas Shtrikman, Nature 385, 417 (1997)] reported the measurement of the transmission phase of an electron traversing a quantum dot and found the intriguing feature of a sudden phase drop in the conductance valleys. Based on the Friedel sum rule for a spinless effective one-dimensional system, it has been previously argued [H.-W. Lee, Phys. Rev. Lett. 82, 2358 (1999)] that the sudden phase drop should be accompanied by the vanishing of the transmission amplitude, or transmission zero. Here we address roles of strong electron-electron interactions on the electron transport through a two-level quantum dot where one level couples with the leads much more strongly than the other level does [P. G. Silvestrov and Y. Imry, Phys. Rev. Lett. 85, 2565 (2000)]. We perform a perturbative conductance calculation with an explicit account of large charging energy and verify that the resulting conductance exhibits transmission zero, in agreement with the analysis based on the Friedel sum rule.
First principles calculation of thermo-mechanical properties of thoria using Quantum ESPRESSO
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.
Energy Technology Data Exchange (ETDEWEB)
Burkatzki, Mark Thomas
2008-07-01
The author presents scalar-relativistic energy-consistent Hartree-Fock pseudopotentials for the main-group and 3d-transition-metal elements. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. The author demonstrates their transferability through extensive benchmark calculations of atomic excitation spectra as well as molecular properties. In particular, the author computes the vibrational frequencies and binding energies of 26 first- and second-row diatomic molecules using post Hartree-Fock methods, finding excellent agreement with the corresponding all-electron values. The author shows that the presented pseudopotentials give superior accuracy than other existing pseudopotentials constructed specifically for QMC. The localization error and the efficiency in QMC are discussed. The author also presents QMC calculations for selected atomic and diatomic 3d-transitionmetal systems. Finally, valence basis sets of different sizes (VnZ with n=D,T,Q,5 for 1st and 2nd row; with n=D,T for 3rd to 5th row; with n=D,T,Q for the 3d transition metals) optimized for the pseudopotentials are presented. (orig.)
Quantum chemical treatment of nivalenol and its tautomers
Energy Technology Data Exchange (ETDEWEB)
Tuerker, Lemi [Middle East Technical University, Department of Chemistry, 06531 Ankara (Turkey)], E-mail: lturker@metu.edu.tr; Guemues, Selcuk [Middle East Technical University, Department of Chemistry, 06531 Ankara (Turkey)
2008-05-01
Nivalenol, a highly poisonous mycotoxin, and its possible tautomers have been considered theoretically by RHF/6-31G/d,p) and B3LYP/6-31G(d,p) calculations together with a semi-empirical PM3 method. The calculations revealed that some of the tautomers are more stable and exothermic than nivalenol. The calculated IR spectra as well as some geometrical and physicochemical properties of the structures considered have been presented.
Breuer, H P; Petruccione, F; Breuer, Heinz-Peter; Kappler, Bernd; Petruccione, Francesco
1997-01-01
Within the framework of probability distributions on projective Hilbert space a scheme for the calculation of multitime correlation functions is developed. The starting point is the Markovian stochastic wave function description of an open quantum system coupled to an environment consisting of an ensemble of harmonic oscillators in arbitrary pure or mixed states. It is shown that matrix elements of reduced Heisenberg picture operators and general time-ordered correlation functions can be expressed by time-symmetric expectation values of extended operators in a doubled Hilbert space. This representation allows the construction of a stochastic process in the doubled Hilbert space which enables the determination of arbitrary matrix elements and correlation functions. The numerical efficiency of the resulting stochastic simulation algorithm is investigated and compared with an alternative Monte Carlo wave function method proposed first by Dalibard et al. [Phys. Rev. Lett. {\\bf 68}, 580 (1992)]. By means of a stan...
A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data
Eckl, Bernhard; Hasse, Hans
2009-01-01
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...
Directory of Open Access Journals (Sweden)
A A Shokri
2013-10-01
Full Text Available In this paper, we have investigated the spin-dependent transport properties and electron entanglement in a mesoscopic system, which consists of two semi-infinite leads (as source and drain separated by a typical quantum wire with a given potential. The properties studied include current-voltage characteristic, electrical conductivity, Fano factor and shot noise, and concurrence. The calculations are based on the transfer matrix method within the effective mass approximation. Using the Landauer formalism and transmission coefficient, the dependence of the considered quantities on type of potential well, length and width of potential well, energy of transmitted electron, temperature and the voltage have been theoretically studied. Also, the effect of the above-mentioned factors has been investigated in the nanostructure. The application of the present results may be useful in designing spintronice devices.
arXiv Axion-photon conversion caused by dielectric interfaces: quantum field calculation
Ioannisian, Ara N.; Millar, Alexander J.; Raffelt, Georg G.
2017-09-05
Axion-photon conversion at dielectric interfaces, immersed in a near-homogeneous magnetic field, is the basis for the dielectric haloscope method to search for axion dark matter. In analogy to transition radiation, this process is possible because the photon wave function is modified by the dielectric layers ("Garibian wave function") and is no longer an eigenstate of momentum. A conventional first-order perturbative calculation of the transition probability between a quantized axion state and these distorted photon states provides the microwave production rate. It agrees with previous results based on solving the classical Maxwell equations for the combined system of axions and electromagnetic fields. We argue that in general the average photon production rate is given by our result, independently of the detailed quantum state of the axion field. Moreover, our result provides a new perspective on axion-photon conversion in dielectric haloscopes because the rate is based on an overlap integral between unpertu...
Quantum-mechanical calculations of cross sections for electron collisions with atoms and molecules
Bartschat, Klaus; Zatsarinny, Oleg
2016-01-01
An overview of quantum-mechanical methods to generate cross-section data for electron collisions with atoms and molecules is presented. Particular emphasis is placed on the time-independent close-coupling approach, since it is particularly suitable for low-energy collisions and also allows for systematic improvements as well as uncertainty estimates. The basic ideas are illustrated with examples for electron collisions with argon atoms and methane. For many atomic systems, such as e-Ar collisions, highly reliable cross sections can now be computed with quantified uncertainties. On the other hand, while electron collision calculations with molecules do provide key input data for plasma models, the methods and computer codes presently used require further development to make these inputs robust.
Directory of Open Access Journals (Sweden)
Dwyer Donard S
2005-08-01
Full Text Available Abstract Background Electronic properties of amino acid side chains such as inductive and field effects have not been characterized in any detail. Quantum mechanics (QM calculations and fundamental equations that account for substituent effects may provide insight into these important properties. PM3 analysis of electron distribution and polarizability was used to derive quantitative scales that describe steric factors, inductive effects, resonance effects, and field effects of amino acid side chains. Results These studies revealed that: (1 different semiempirical QM methods yield similar results for the electronic effects of side chain groups, (2 polarizability, which reflects molecular deformability, represents steric factors in electronic terms, and (3 inductive effects contribute to the propensity of an amino acid for α-helices. Conclusion The data provide initial characterization of the substituent effects of amino acid side chains and suggest that these properties affect electron density along the peptide backbone.
Frozen-orbital and downfolding calculations with auxiliary-field quantum Monte Carlo
Purwanto, Wirawan; Krakauer, Henry
2013-01-01
We describe the implementation of the frozen-orbital and downfolding approximations in the auxiliary-field quantum Monte Carlo (AFQMC) method. These approaches can provide significant computational savings compared to fully correlating all the electrons. While the many-body wave function is never explicit in AFQMC, its random walkers are Slater determinants, whose orbitals may be expressed in terms of any one-particle orbital basis. It is therefore straightforward to partition the full N-particle Hilbert space into active and inactive parts to implement the frozen-orbital method. In the frozen-core approximation, for example, the core electrons can be eliminated in the correlated part of the calculations, greatly increasing the computational efficiency, especially for heavy atoms. Scalar relativistic effects are easily included using the Douglas-Kroll-Hess theory. Using this method, we obtain a way to effectively eliminate the error due to single-projector, norm-conserving pseudopotentials in AFQMC. We also i...