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McLennan L, Brown‐Nash A, Busby T, Canaria J, Kominia A, Smith JL, Oxley JC, Dubnikov F, Kosloff R, Zeiri Y. Characterization of the Hexanitrate Esters of Sugar Alcohols. Prop , Explos , Pyrotech 2021. [DOI: 10.1002/prep.202000197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lindsay McLennan
- Chemistry Department University of Rhode Island 140 Flagg Road Kingston RI 02881
| | - Audreyana Brown‐Nash
- Chemistry Department University of Rhode Island 140 Flagg Road Kingston RI 02881
| | - Taylor Busby
- Chemistry Department University of Rhode Island 140 Flagg Road Kingston RI 02881
| | - Jeffrey Canaria
- Chemistry Department University of Rhode Island 140 Flagg Road Kingston RI 02881
| | - Athina Kominia
- Chemistry Department University of Rhode Island 140 Flagg Road Kingston RI 02881
| | - James L. Smith
- Chemistry Department University of Rhode Island 140 Flagg Road Kingston RI 02881
| | - Jimmie C. Oxley
- Chemistry Department University of Rhode Island 140 Flagg Road Kingston RI 02881
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2
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Fisher D, Lukow SR, Berezutskiy G, Gil I, Levy T, Zeiri Y. Machine Learning Improves Trace Explosive Selectivity: Application to Nitrate-Based Explosives. J Phys Chem A 2020; 124:9656-9664. [PMID: 33156629 DOI: 10.1021/acs.jpca.0c05909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion mobility spectrometry (IMS) is the method of choice to detect trace amounts of explosives in most airports and border crossing settings. For most explosives, the IMS detection limits are suitably low enough to meet security requirements. However, for some explosive families, the selectivity is not sufficient. One such family is nitrate-based explosives, where discrimination between various nitrate threats and ambient nitrates is challenging. Using a small database, machine learning methods were utilized to examine the extent of improvement in IMS selectivity for detection of nitrate-based explosives. Five classes were considered in this preliminary study: ammonium nitrate (AN), an ∼95:5 mixture of AN and fuel oil (ANFO), urea nitrate (UN), nitrate due to environmental pollution, and samples that did not contain any explosive (blanks). The preliminary results clearly show that the incorporation of machine learning methods can lead to a significant improvement in IMS selectivity.
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Affiliation(s)
- Danny Fisher
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Stefan R Lukow
- Rapiscan Systems, Andover, Massachussetts 01810, United States
| | | | - Itai Gil
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Tal Levy
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yehuda Zeiri
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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3
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4
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Gopas J, Abd EL Qader A, Isaacson C, Eichler D, Zeiri Y. Urine volatile organic compounds composition in mice bearing breast and melanoma tumors: effect of low-protein diet. CBF 2018; Volume 8:1-13. [DOI: 10.2147/cbf.s160340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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5
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Furman D, Carmeli B, Zeiri Y, Kosloff R. Enhanced Particle Swarm Optimization Algorithm: Efficient Training of ReaxFF Reactive Force Fields. J Chem Theory Comput 2018; 14:3100-3112. [PMID: 29727570 DOI: 10.1021/acs.jctc.7b01272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Particle swarm optimization (PSO) is a powerful metaheuristic population-based global optimization algorithm. However, when it is applied to nonseparable objective functions, its performance on multimodal landscapes is significantly degraded. Here we show that a significant improvement in the search quality and efficiency on multimodal functions can be achieved by enhancing the basic rotation-invariant PSO algorithm with isotropic Gaussian mutation operators. The new algorithm demonstrates superior performance across several nonlinear, multimodal benchmark functions compared with the rotation-invariant PSO algorithm and the well-established simulated annealing and sequential one-parameter parabolic interpolation methods. A search for the optimal set of parameters for the dispersion interaction model in the ReaxFF- lg reactive force field was carried out with respect to accurate DFT-TS calculations. The resulting optimized force field accurately describes the equations of state of several high-energy molecular crystals where such interactions are of crucial importance. The improved algorithm also presents better performance compared to a genetic algorithm optimization method in the optimization of the parameters of a ReaxFF- lg correction model. The computational framework is implemented in a stand-alone C++ code that allows the straightforward development of ReaxFF reactive force fields.
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Affiliation(s)
- David Furman
- Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry , Hebrew University of Jerusalem , Jerusalem 91904 , Israel.,Division of Chemistry , NRCN , P.O. Box 9001, Beer-Sheva 84190 , Israel
| | - Benny Carmeli
- Division of Chemistry , NRCN , P.O. Box 9001, Beer-Sheva 84190 , Israel
| | - Yehuda Zeiri
- Department of Biomedical Engineering , Ben Gurion University , Beer-Sheva 94105 , Israel
| | - Ronnie Kosloff
- Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry , Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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6
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Kalson NH, Furman D, Zeiri Y. Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth. ACS Cent Sci 2017; 3:1041-1049. [PMID: 28979946 PMCID: PMC5620973 DOI: 10.1021/acscentsci.7b00325] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 05/03/2023]
Abstract
Despite decades of research, how life began on Earth remains one of the most challenging scientific conundrums facing modern science. It is agreed that the first step was synthesis of organic compounds essential to obtain amino acids and their polymers. Several possible scenarios that could accomplish this step, using simple inorganic molecules, have been suggested and studied over the years. The present study examines, using atomistic reactive molecular dynamics simulations, the long-standing suggestion that natural cavitation in primordial oceans was a dominant mechanism of organic molecule synthesis. The simulations allow, for the first time, direct observation of the rich and complex sonochemistry occurring inside a collapsing bubble filled with water and dissolved gases of the early atmosphere. The simulation results suggest that dissolved CH4 is the most efficient carbon source to produce amino acids, while CO and CO2 lead to amino acid synthesis with lower yields. The efficiency of amino acid synthesis also depends on the nitrogen source used (i.e., N2, NH3) and on the presence of HCN. Moreover, cavitation may have contributed to the increase in concentration of NH3 in primordial oceans and to the production and liberation of molecular O2 into the early atmosphere. Overall, the picture that emerges from the simulations indicates that collapsing bubbles may have served as natural bioreactors in primordial oceans, producing the basic chemical ingredients required for the beginning of life.
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Affiliation(s)
- Natan-Haim Kalson
- Biomedical
Engineering, Ben-Gurion University of the
Negev, Beer-Sheva 84105, Israel
- The
Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes
for Desert Research, Ben-Gurion University
of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion 8499000, Israel
| | - David Furman
- Fritz
Haber Research Center for Molecular Dynamics, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Division
of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel
| | - Yehuda Zeiri
- Biomedical
Engineering, Ben-Gurion University of the
Negev, Beer-Sheva 84105, Israel
- Division
of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel
- E-mail:
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7
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Cohen D, Merchuk J, Zeiri Y, Sadot O. Catalytic effectiveness of porous particles: A continuum analytic model including internal and external surfaces. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.03.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fisher D, Zach R, Matana Y, Elia P, Shustack S, Sharon Y, Zeiri Y. Bomb swab: Can trace explosive particle sampling and detection be improved? Talanta 2017; 174:92-99. [PMID: 28738664 DOI: 10.1016/j.talanta.2017.05.085] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/28/2017] [Accepted: 05/29/2017] [Indexed: 11/29/2022]
Abstract
The marked increase in international terror in recent years requires the development of highly efficient methods to detect trace amounts of explosives at airports, border crossings and check points. The preferred analytical method worldwide is the ion mobility spectrometry (IMS) that is capable of detecting most explosives at the nano-gram level. Sample collection for the IMS analysis is based on swabbing of a passenger's belongings to collect possible explosive residues. The present study examines a wide range of issues related to swab-based particle collection and analysis, in the hope of gaining deeper understanding into this technique that will serve to improve the detection process. The adhesion of explosive particles to three typical materials, plastic, metal and glass, were measured using atomic force microscopy (AFM). We found that a strong contribution of capillary forces to adhesion on glass and metal surfaces renders these substrates more promising materials upon which to find and collect explosive residues. The adhesion of explosives to different swipe materials was also examined. Here we found that Muslin, Nomex® and polyamide membrane surfaces are the most promising materials for use as swipes. Subsequently, the efficiency of multiple swipe use - for collecting explosive residues from a glass surface using Muslin, Nomex® and Teflon™ swipes - was examined. The study suggests that swipes used in about 5-10 "sampling and analysis cycles" have higher efficiency as compared to new unused swipes. The reason for this behavior was found to be related to the increased roughness of the swipe surface following a few swab measurements. Lastly, GC-MS analysis was employed to examine the nature of contaminants collected by the three types of swipe. The relative amounts of different contaminants are reported. The existence and interference of these contaminants have to be considered in relation to the detection efficiency of the various explosives by the IMS.
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Affiliation(s)
- Danny Fisher
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Raya Zach
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yossef Matana
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Paz Elia
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shiran Shustack
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yarden Sharon
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yehuda Zeiri
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Division of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva, Israel.
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9
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Sela H, Cohen H, Karpas Z, Zeiri Y. Correction: Distinctive hippocampal zinc distribution patterns following stress exposure in an animal model of PTSD. Metallomics 2017; 9:584. [PMID: 28489098 DOI: 10.1039/c7mt90018j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correction for 'Distinctive hippocampal zinc distribution patterns following stress exposure in an animal model of PTSD' by Hagit Sela et al., Metallomics, 2017, 9, 323-333.
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Affiliation(s)
- Hagit Sela
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
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10
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Sela H, Cohen H, Karpas Z, Zeiri Y. Distinctive hippocampal zinc distribution patterns following stress exposure in an animal model of PTSD. Metallomics 2017; 9:323-333. [PMID: 28252129 DOI: 10.1039/c6mt00207b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Emerging evidence suggests that zinc (Zn) deficiency is associated with depression and anxiety in both human and animal studies. The present study sought to assess whether there is an association between the magnitude of behavioral responses to stress and patterns of Zn distribution. The work has focused on one case study, the association between an animal model of posttraumatic stress disorder (PTSD) and the Zn distribution in the rat hippocampus. Behaviors were assessed with the elevated plus-maze and acoustic startle response tests 7 days later. Preset cut-off criteria classified exposed animals according to their individual behavioral responses. To further characterize the distribution of Zn that occurs in the hippocampus 8 days after the exposure, laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging was used. It has been found that Zn distribution in the dentate gyrus (DG) sub-region in the hippocampus is clearly more widely spread for rats that belong to the extreme behavioral response (EBR) group as compared to the control group. Comparison of the Zn concentration changes in the cornu ammonis 1 (CA1) and the DG sub-regions of the hippocampus shows that the concentration changes are statistically significantly higher in the EBR rats compared to the rats in the control and minimal behavioral response (MBR) groups. In order to understand the mechanism of stress-induced hippocampal Zn dyshomeostasis, relative quantitative analyses of metallothionein (MT), B-cell lymphoma 2 (Bcl-2) and caspase 3 immunoreactivity were performed. Significant differences in the number of caspase-ir and Bcl-2 cells were found in the hippocampal DG sub-region between the EBR group and the control and MBR groups. The results of this study demonstrate a statistically significant association between the degree of behavioral disruption resulting from stress exposure and the patterns of Zn distribution and concentration changes in the various hippocampal regions. Taken together, these findings indicate that Zn distribution patterns play an active role in the neurobiological response to predator scent stress.
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Affiliation(s)
- Hagit Sela
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel. and Department of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 8419001, Israel.
| | - Hagit Cohen
- Beer-Sheva Mental Health Center, The State of Israel Ministry of Health, Anxiety and Stress Research Unit, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Zeev Karpas
- Department of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 8419001, Israel.
| | - Yehuda Zeiri
- Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel. and Department of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 8419001, Israel.
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11
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Oxley JC, Smith JL, Porter M, McLennan L, Colizza K, Zeiri Y, Kosloff R, Dubnikova F. Synthesis and Degradation of Hexamethylene Triperoxide Diamine (HMTD). Propellants, Explosives, Pyrotechnics 2015. [DOI: 10.1002/prep.201500151] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Affiliation(s)
- Faina Dubnikova
- The
Fritz Haber Research Center for Molecular Dynamics, The Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yehuda Zeiri
- Division
of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel
- Biomedical
Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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13
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Sela H, Cohen H, Elia P, Zach R, Karpas Z, Zeiri Y. Spontaneous penetration of gold nanoparticles through the blood brain barrier (BBB). J Nanobiotechnology 2015; 13:71. [PMID: 26489846 PMCID: PMC4618365 DOI: 10.1186/s12951-015-0133-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 10/06/2015] [Indexed: 01/17/2023] Open
Abstract
Background The blood brain barrier (BBB) controls the brain microenvironment and limits penetration of the central nervous system (CNS) by chemicals, thus creating an obstacle to many medical imaging and treatment procedures. Research efforts to identify viable routes of BBB penetration have focused on structures such as micelles, polymeric nanoparticles and liposomes as drug carriers, however, many of them failed to provide unequivocal proof of BBB penetration. Here we proved that gold nanoparticles (AuNPs) penetrate the BBB in rats to reach brain regions. Results Injection of AuNPs to the abdominal cavity of rats resulted in levels of gold found in blood, urine, brain regions and body organs. After perfusion the concentration of gold in brain regions diminished dramatically indicating that most of the gold was in venous blood and not in the brain tissues. Injection of Na, K or Ca ion channel blockers reduced BBB penetration by half. A biological half-life of 12.9 ± 4.9 h was found for the gold nanoparticles. Possible mechanisms for the transport of AuNPs through the BBB are discussed. Conclusions BBB penetration by AuNPs is spontaneous without the application of an external field. A major amount of gold resides in blood vessels therefore perfusion required. Ion channel blockers can be used to control the transport of AuNPs. Electronic supplementary material The online version of this article (doi:10.1186/s12951-015-0133-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hagit Sela
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel. .,Department of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva, 8419001, Israel.
| | - Hagit Cohen
- The State of Israel Ministry of Health, Anxiety and Stress Research Unit, Faculty of Health Sciences, Beer-Sheva Mental Health Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Paz Elia
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
| | - Raya Zach
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
| | - Zeev Karpas
- Department of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva, 8419001, Israel.
| | - Yehuda Zeiri
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel. .,Department of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva, 8419001, Israel.
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14
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Cohen D, Nahmani M, Rafailov G, Attia S, Shamish Z, Landau M, Merchuk J, Zeiri Y. Oxidation mechanism of porous Zr₂Fe used as a hydrogen getter. Appl Radiat Isot 2015; 107:47-56. [PMID: 26408914 DOI: 10.1016/j.apradiso.2015.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/31/2015] [Accepted: 09/05/2015] [Indexed: 10/23/2022]
Abstract
We determined the oxidation mechanism of porous ST-198, which mainly comprises Zr2Fe. Oxidation kinetics depended on temperature, oxygen partial pressure, and oxidation extent. The passivation role of oxidation in hydrogen scavenging is probably due to the development of a surface oxide, independent of oxygen concentration. Zr2Fe would be a superior hydrogen getter in oxygen-contaminated environments at high temperatures, as most oxygen will be consumed at the outer shell by mass transfer limitations, protecting the bulk of the getter for hydrogen scavenging.
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Affiliation(s)
- Dror Cohen
- Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; Nuclear Research Centre-Negev, P.O. Box 9001, Beer-Sheva 84190, Israel.
| | - Moshe Nahmani
- Nuclear Research Centre-Negev, P.O. Box 9001, Beer-Sheva 84190, Israel
| | - Genadi Rafailov
- Nuclear Research Centre-Negev, P.O. Box 9001, Beer-Sheva 84190, Israel
| | - Smadar Attia
- Israel Atomic Energy Commission, Tel Aviv 61070, Israel
| | - Zorik Shamish
- Nuclear Research Centre-Negev, P.O. Box 9001, Beer-Sheva 84190, Israel
| | - Miron Landau
- Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Jose Merchuk
- Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yehuda Zeiri
- Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; Nuclear Research Centre-Negev, P.O. Box 9001, Beer-Sheva 84190, Israel
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15
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Abd El Qader A, Lieberman D, Shemer Avni Y, Svobodin N, Lazarovitch T, Sagi O, Zeiri Y. Volatile organic compounds generated by cultures of bacteria and viruses associated with respiratory infections. Biomed Chromatogr 2015; 29:1783-90. [PMID: 26033043 DOI: 10.1002/bmc.3494] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/06/2015] [Accepted: 04/13/2015] [Indexed: 11/09/2022]
Abstract
Respiratory infections (RI) can be viral or bacterial in origin. In either case, the invasion of the pathogen results in production and release of various volatile organic compounds (VOCs). The present study examines the VOCs released from cultures of five viruses (influenza A, influenza B, adenovirus, respiratory syncitial virus and parainfluenza 1 virus), three bacteria (Moraxella catarrhalis, Haemophilus influenzae and Legionella pneumophila) and Mycoplasma pneumoniae isolated colonies. Our results demonstrate the involvement of inflammation-induced VOCs. Two significant VOCs were identified as associated with infectious bacterial activity, heptane and methylcyclohexane. These two VOCs have been linked in previous studies to oxidative stress effects. In order to distinguish between bacterial and viral positive cultures, we performed principal component analysis including peak identity (retention time) and VOC concentration (i.e. area under the peak) revealing 1-hexanol and 1-heptadecene to be good predictors.
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Affiliation(s)
- Amir Abd El Qader
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - David Lieberman
- Pulmonary Unit, Soroka University Medical Center and the Faculty of Health, Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yonat Shemer Avni
- The Laboratory of Viral Diagnostics, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Natali Svobodin
- The Laboratory of Viral Diagnostics, Soroka University Medical Center, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Tsilia Lazarovitch
- Department of Clinical Microbiology, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Orli Sagi
- Parasitology Laboratory, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yehuda Zeiri
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Division of Chemistry, Nuclear Research Center, Negev, Beer-Sheva, Israel
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16
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Abstract
Gold nanoparticles (GNPs) were prepared using four different plant extracts as reducing and stabilizing agents. The extracts were obtained from the following plants: Salvia officinalis, Lippia citriodora, Pelargonium graveolens and Punica granatum. The size distributions of the GNPs were measured using three different methods: dynamic light scattering, nanoparticle-tracking analysis and analysis of scanning electron microscopy images. The three methods yielded similar size distributions. Biocompatibility was examined by correlation of L-cell growth in the presence of different amounts of GNPs. All GNPs showed good biocompatibility and good stability for over 3 weeks. Therefore, they can be used for imaging and drug-delivery applications in the human body. High-resolution transmission electron microscopy was used to view the shapes of the larger GNPs, while infrared spectroscopy was employed to characterize the various functional groups in the organic layer that stabilize the particles. Finally, active ingredients in the plant extract that might be involved in the formation of GNPs are proposed, based on experiments with pure antioxidants that are known to exist in that plant.
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Affiliation(s)
- Paz Elia
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Israel
| | - Raya Zach
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Israel
| | - Sharon Hazan
- Ilse Katz Institute of Nanotechnology, Ben-Gurion University of the Negev, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute of Nanotechnology, Ben-Gurion University of the Negev, Israel
| | - Ze'ev Porat
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Israel ; Division of Chemistry, Negev Nuclear Research Center Beersheba, Israel
| | - Yehuda Zeiri
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Israel ; Division of Chemistry, Negev Nuclear Research Center Beersheba, Israel
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17
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Furman D, Kosloff R, Dubnikova F, Zybin SV, Goddard WA, Rom N, Hirshberg B, Zeiri Y. Decomposition of condensed phase energetic materials: interplay between uni- and bimolecular mechanisms. J Am Chem Soc 2014; 136:4192-200. [PMID: 24495109 DOI: 10.1021/ja410020f] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Activation energy for the decomposition of explosives is a crucial parameter of performance. The dramatic suppression of activation energy in condensed phase decomposition of nitroaromatic explosives has been an unresolved issue for over a decade. We rationalize the reduction in activation energy as a result of a mechanistic change from unimolecular decomposition in the gas phase to a series of radical bimolecular reactions in the condensed phase. This is in contrast to other classes of explosives, such as nitramines and nitrate esters, whose decomposition proceeds via unimolecular reactions both in the gas and in the condensed phase. The thermal decomposition of a model nitroaromatic explosive, 2,4,6-trinitrotoluene (TNT), is presented as a prime example. Electronic structure and reactive molecular dynamics (ReaxFF-lg) calculations enable to directly probe the condensed phase chemistry under extreme conditions of temperature and pressure, identifying the key bimolecular radical reactions responsible for the low activation route. This study elucidates the origin of the difference between the activation energies in the gas phase (~62 kcal/mol) and the condensed phase (~35 kcal/mol) of TNT and identifies the corresponding universal principle. On the basis of these findings, the different reactivities of nitro-based organic explosives are rationalized as an interplay between uni- and bimolecular processes.
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Affiliation(s)
- David Furman
- Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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18
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Katz G, Zybin S, Goddard WA, Zeiri Y, Kosloff R. Direct MD Simulations of Terahertz Absorption and 2D Spectroscopy Applied to Explosive Crystals. J Phys Chem Lett 2014; 5:772-776. [PMID: 26274066 DOI: 10.1021/jz402801m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A direct molecular dynamics simulation of the THz spectrum of a molecular crystal is presented. A time-dependent electric field is added to a molecular dynamics simulation of a crystal slab. The absorption spectrum is composed from the energy dissipated calculated from a series of applied pulses characterized by a carrier frequency. The spectrum of crystalline cyclotrimethylenetrinitramine (RDX) and triacetone triperoxide (TATP) were simulated with the ReaxFF force field. The proposed direct method avoids the linear response and harmonic approximations. A multidimensional extension of the spectroscopy is suggested and simulated based on the nonlinear response to a single polarized pulse of radiation in the perpendicular polarization direction.
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Affiliation(s)
- G Katz
- †Fritz Haber Research Center for Molecular Dynamics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - S Zybin
- ‡Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - W A Goddard
- ‡Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Y Zeiri
- ¶Chemistry Department, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel
- §Bio-Medical Engineering, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - R Kosloff
- †Fritz Haber Research Center for Molecular Dynamics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Sela H, Karpas Z, Cohen H, Tal A, Zeiri Y. Trace element concentration in hair samples as an indicator of exposure of population in the Negev, Israel. Biol Trace Elem Res 2013; 155:209-20. [PMID: 23975582 DOI: 10.1007/s12011-013-9794-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022]
Abstract
The concentration of the toxic elements Ag, As, Cd, Co, Mn, Mo, Pb, Se, and U and the elements Al, Mg, Cu, Fe, and Zn in human hair samples of population living in the north of the Negev Desert in Israel was determined. The study population consisted of three subgroups: Jewish urban population, Bedouin urban population, and Bedouins living in unrecognized villages (the "dispersion"). The main focus is on the differences between these subgroups in an attempt to explore factors responsible for the variation in trace metal contents in hair samples. The results show that the level of several elements, particularly Ag, Mn, and Pb, in the female Bedouin group significantly differed from the other groups in the study. Exploring the reasons for these differences, we concluded that the lifestyle of those women is the main cause. The female Bedouin subgroup is exposed to heavy metals from kitchen utensils, jewelry, and makeup. Therefore, differences in the heavy metal concentration in the hair samples of this group were attributed to the traditional unique lifestyle and social behavior of the females in the Bedouin society.
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Affiliation(s)
- H Sela
- Department of Chemistry, Nuclear Research Center, Negev, P.O. Box 9001, Beer-Sheva, 84190, Israel,
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21
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Elia P, Azoulay A, Zeiri Y. On the efficiency of water soluble antioxidants. Ultrason Sonochem 2012; 19:314-324. [PMID: 21798788 DOI: 10.1016/j.ultsonch.2011.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/03/2011] [Accepted: 01/05/2011] [Indexed: 05/31/2023]
Abstract
The wide use of high intensity ultrasound (HIU) in modern medicine raises the question of bio-safety. It has been shown that the effect of HIU in biological media may have similarity to the effects of ionizing radiation. Exposure of biological media to HIU field may lead to cavitation phenomenon followed by formation of free radicals such as hydroxyl radical (OH(·)) and the super-oxide ion (O(2)(·-)). These are highly reactive species that may cause harmful effects and induce oxidative stress. In the present study we employed electron spin resonance (ESR) spectroscopy together with spin traps to quantify the dynamics of hydroxyl radical formation during exposure to HIU field in the presence of different amounts of six antioxidants. Thus, the efficiency of water-soluble antioxidants, namely Allicin, Melatonin, Deoxyribose, Trolox, Nuphlutine and Hermidin, to suppress accumulation of OH radicals was examined. The results show that among the six, Trolox and Allicin reduce hydroxyl concentration with the highest efficiency.
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Affiliation(s)
- Paz Elia
- Biomedical Engineering, Ben-Gurion University, Beer-Sheva 84105, Israel
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22
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Zeiri L, Rechav K, Porat Z, Zeiri Y. Silver nanoparticles deposited on porous silicon as a surface-enhanced Raman scattering (SERS) active substrate. Appl Spectrosc 2012; 66:294-299. [PMID: 22449306 DOI: 10.1366/11-06476] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Silver nanoparticles were deposited spontaneously from their aqueous solution on a porous silicon (PS) layer. The PS acts both as a reducing agent and as the substrate on which the nanoparticles nucleate. At higher silver ion concentrations, layers of nanoparticle aggregates were formed on the PS surface. The morphology of the metallic layers and their SERS activity were influenced by the concentrations of the silver ion solutions used for deposition. Raman measurements of rhodamine 6G (R6G) and crystal violet (CV) adsorbed on these surfaces showed remarkable enhancement of up to about 10 orders of magnitude.
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Affiliation(s)
- Leila Zeiri
- Department of Chemistry, Ben-Gurion University, Be'er-Sheva 84105, Israel
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Oxley JC, Smith JL, Kirschenbaum LJ, Marimiganti S, Efremenko I, Zach R, Zeiri Y. Accumulation of explosives in hair--Part 3: Binding site study. J Forensic Sci 2012; 57:623-35. [PMID: 22235760 DOI: 10.1111/j.1556-4029.2011.02020.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study extends previous work on the sorption of explosives to the hair matrix. Specifically, we have studied the interaction of 2,4,6-trinitrotoluene (TNT) and triacetone triperoxide (TATP) as a function of chemical pretreatment with acetonitrile, neutral and alkaline hydrogen peroxide, methanolic KOH and potassium permanganate, and the morphological changes that accompany these treatments. While differences in vapor pressure can account for quantitative differences between TNT and TATP sorption, both are markedly affected by the chemical rinses. Examination of the hair surface shows different degrees of smoothening following rinsing, suggesting that the attachment to hair is largely a surface phenomenon involving the 18-methyleicosanoic acid lipid layer. Density functional theory calculations were employed to explore possible nucleation sites of TATP microcrystals on the hair. We conclude that some of the sites on melanin granular surfaces may support nucleation of TATP microcrystals. Moreover, the calculations support the experimental finding that dark hair adsorbs explosives better than light hair.
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Affiliation(s)
- Jimmie C Oxley
- Department of Chemistry, University of Rhode Island, Kingston, RI 02881, USA.
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24
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Pinchas M, Zeiri Y, Hoz S. Nano-molecular springs: How high will it jump? COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Am-Shallem M, Zeiri Y, Zybin SV, Kosloff R. Molecular dynamics simulations of weak detonations. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 84:061122. [PMID: 22304055 DOI: 10.1103/physreve.84.061122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 10/31/2011] [Indexed: 05/31/2023]
Abstract
Detonation of a three-dimensional reactive nonisotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave. The terminal shock velocity is independent of the initiation conditions. Further analysis shows supersonic propagation decoupled from the dynamics of the decomposed material left behind the shock front. The dependence of the shock velocity on crystal nonlinear compressibility resembles solitary behavior. These properties categorize the phenomena as a weak detonation. The dependence of the detonation wave on microscopic potential parameters was investigated. An increase in detonation velocity with the reaction exothermicity reaching a saturation value is observed. In all other respects the model crystal exhibits typical properties of a molecular crystal.
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Affiliation(s)
- Morag Am-Shallem
- Fritz Haber Research Center, Hebrew University, Jerusalem 91904, Israel
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Dubnikova F, Kosloff R, Oxley JC, Smith JL, Zeiri Y. Role of Metal Ions in the Destruction of TATP: Theoretical Considerations. J Phys Chem A 2011; 115:10565-75. [DOI: 10.1021/jp2021616] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Faina Dubnikova
- Institute of Chemistry, Hebrew University, Jerusalem, Israel
| | - Ronnie Kosloff
- Institute of Chemistry, Hebrew University, Jerusalem, Israel
| | - Jimmie C. Oxley
- Chemistry Department, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - James L. Smith
- Chemistry Department, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Yehuda Zeiri
- Chemistry Division, Nuclear Research Center−Negev, P.O. Box 9001 Beer-Sheva, 84190 Israel
- Biomedical Engineering, Ben-Gurion University, Beer-Sheva, 84105 Israel
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27
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Rom N, Zybin SV, van Duin ACT, Goddard WA, Zeiri Y, Katz G, Kosloff R. Density-Dependent Liquid Nitromethane Decomposition: Molecular Dynamics Simulations Based on ReaxFF. J Phys Chem A 2011; 115:10181-202. [DOI: 10.1021/jp202059v] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Naomi Rom
- Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
| | - Sergey V. Zybin
- Materials and Process Simulation Center, 139-74, California Institute of Technology, Pasadena, California 91125, United States
| | - Adri C. T. van Duin
- Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - William A. Goddard
- Materials and Process Simulation Center, 139-74, California Institute of Technology, Pasadena, California 91125, United States
| | - Yehuda Zeiri
- Bio-medical Engineering, Ben Gurion University, Beer-Sheva 84105, Israel
- Division of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel
| | - Gil Katz
- Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
| | - Ronnie Kosloff
- Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
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Affiliation(s)
- Arcady P. Gershanik
- Biomedical Engineering, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel, and Division of Chemistry, NRCN, Beer-Sheva P.O. Box 9001, 84190, Israel
| | - Yehuda Zeiri
- Biomedical Engineering, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel, and Division of Chemistry, NRCN, Beer-Sheva P.O. Box 9001, 84190, Israel
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Marom R, Levi C, Weiss T, Rosenwaks S, Zeiri Y, Kosloff R, Bar I. Quantum Tunneling of Hydrogen Atom in Dissociation of Photoexcited Methylamine. J Phys Chem A 2010; 114:9623-7. [DOI: 10.1021/jp912107h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ran Marom
- Department of Physics, Ben-Gurion University, Beer Sheva 84105, Israel, Department of Biomedical Engineering, Ben-Gurion University, Beer Sheva 84105, Israel and Department of Chemistry, NRCN, Beer-Sheva 84190, Israel, Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chen Levi
- Department of Physics, Ben-Gurion University, Beer Sheva 84105, Israel, Department of Biomedical Engineering, Ben-Gurion University, Beer Sheva 84105, Israel and Department of Chemistry, NRCN, Beer-Sheva 84190, Israel, Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tal Weiss
- Department of Physics, Ben-Gurion University, Beer Sheva 84105, Israel, Department of Biomedical Engineering, Ben-Gurion University, Beer Sheva 84105, Israel and Department of Chemistry, NRCN, Beer-Sheva 84190, Israel, Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Salman Rosenwaks
- Department of Physics, Ben-Gurion University, Beer Sheva 84105, Israel, Department of Biomedical Engineering, Ben-Gurion University, Beer Sheva 84105, Israel and Department of Chemistry, NRCN, Beer-Sheva 84190, Israel, Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yehuda Zeiri
- Department of Physics, Ben-Gurion University, Beer Sheva 84105, Israel, Department of Biomedical Engineering, Ben-Gurion University, Beer Sheva 84105, Israel and Department of Chemistry, NRCN, Beer-Sheva 84190, Israel, Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ronnie Kosloff
- Department of Physics, Ben-Gurion University, Beer Sheva 84105, Israel, Department of Biomedical Engineering, Ben-Gurion University, Beer Sheva 84105, Israel and Department of Chemistry, NRCN, Beer-Sheva 84190, Israel, Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University, Beer Sheva 84105, Israel, Department of Biomedical Engineering, Ben-Gurion University, Beer Sheva 84105, Israel and Department of Chemistry, NRCN, Beer-Sheva 84190, Israel, Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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30
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Levi C, Halász GJ, Vibók A, Bar I, Zeiri Y, Kosloff R, Baer M. Intralines of quasi-conical intersections on torsion planes: methylamine as a case study. J Phys Chem A 2009; 113:6756-62. [PMID: 19462985 DOI: 10.1021/jp901072u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently we reported on a novel feature associated with the intersection of the two lowest states (1)A' and (1)A'' of the methylamine (J. Chem. Phys. 2008, 128, 244302). We established the existence of a finite (closed) line of conical intersections (ci), namely, a finite seam, located in the HC-NHH symmetry plane, a line that is formed by moving a single hydrogen on that plane while locking the positions of the (six) other atoms. In the present article, this study is extended to the corresponding torsion planes formed by rotating the methyl group around the CN axis. The torsion planes, in contrast with the HC-NHH symmetry plane, do not satisfy the symmetry feature that enables the seam just mentioned. Nevertheless, the calculated nonadiabatic coupling terms (NACTs) resemble features similar to those encountered in the HC-NHH symmetry plane. Following a tedious numerical study supported by a theoretical model (Section III), it was verified that these NACTs may become similar to those on the symmetry plane, sometimes even to the level of almost no distinction, but lack one basic feature; namely, they are not singular and therefore do not form topological effects.
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Affiliation(s)
- C Levi
- Department of Physics, Ben-Gurion University, Beer Sheva, 84105, Israel
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Levi C, Kosloff R, Zeiri Y, Bar I. Time-dependent quantum wave-packet description of H and D atom tunneling in N–H and N–D photodissociation of methylamine and methylamine-d[sub 2]. J Chem Phys 2009; 131:064302. [DOI: 10.1063/1.3204000] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Brauer B, Dubnikova F, Zeiri Y, Kosloff R, Gerber RB. Vibrational spectroscopy of triacetone triperoxide (TATP): anharmonic fundamentals, overtones and combination bands. Spectrochim Acta A Mol Biomol Spectrosc 2008; 71:1438-1445. [PMID: 18554978 DOI: 10.1016/j.saa.2008.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Revised: 04/14/2008] [Accepted: 04/22/2008] [Indexed: 05/26/2023]
Abstract
The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm(-1) region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed.
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Affiliation(s)
- Brina Brauer
- Department of Physical Chemistry and Fritz Haber Institute for Molecular Dynamics, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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Oxley J, Smith J, Brady J, Dubnikova F, Kosloff R, Zeiri L, Zeiri Y. Raman and infrared fingerprint spectroscopy of peroxide-based explosives. Appl Spectrosc 2008; 62:906-15. [PMID: 18702865 DOI: 10.1366/000370208785284420] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A comparative study of the vibrational spectroscopy of peroxide-based explosives is presented. Triacetone triperoxide (TATP) and hexamethyl-enetriperoxide-diamine (HMTD), now commonly used by terrorists, are examined as well as other peroxide-ring structures: DADP (diacetone diperoxide); TPTP [3,3,6,6,9,9-Hexaethyl-1,2,4,5,7,8-hexaoxo-nonane (tripentanone triperoxide)]; DCypDp {6,7,13,14-Tetraoxadispiro [4.2.4.2]tetradecane (dicyclopentanone diperoxide)}; TCypDp {6,7,15,16,22,23-Hexaoxatrispiro[4.2.4.2.4.2] henicosane (tricyclopentanone triperoxide)}; DCyhDp {7,8,15,16-tetraoxadispiro [5.2.5.2] hexadecane (dicyclohexanone diperoxide)}; and TCyhTp {7,8,14,15,21,22-hexaoxatrispiro [5.2.5.2.5.2] tetracosane (tricyclohexanone triperoxide)}. Both Raman and infrared (IR) spectra were measured and compared to theoretical calculations. The calculated spectra were obtained by calculation of the harmonic frequencies of the studied compounds, at the density functional theory (DFT) B3LYP/cc-pVDZ level of theory, and by the use of scaling factors. It is found that the vibrational features related to the peroxide bonds are strongly mixed. As a result, the spectrum is congested and highly sensitive to minor changes in the molecule.
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Affiliation(s)
- Jimmie Oxley
- Chemistry Department, University of Rhode Island, Kingston, Rhode Island, USA.
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Levi C, Halász GJ, Vibók Á, Bar I, Zeiri Y, Kosloff R, Baer M. An intraline of conical intersections for methylamine. J Chem Phys 2008; 128:244302. [DOI: 10.1063/1.2943143] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Cohen R, Zeiri Y, Wurzberg E, Kosloff R. Mechanism of Thermal Unimolecular Decomposition of TNT (2,4,6-Trinitrotoluene): A DFT Study. J Phys Chem A 2007; 111:11074-83. [DOI: 10.1021/jp072121s] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Revital Cohen
- Chemical Research Support Unit, Department of Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel, Chemistry Department, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel, Rafael Intelligence and Security Directorate, P.O. Box 2250, Haifa, 31021, Israel, and Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
| | - Yehuda Zeiri
- Chemical Research Support Unit, Department of Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel, Chemistry Department, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel, Rafael Intelligence and Security Directorate, P.O. Box 2250, Haifa, 31021, Israel, and Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
| | - Elhanan Wurzberg
- Chemical Research Support Unit, Department of Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel, Chemistry Department, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel, Rafael Intelligence and Security Directorate, P.O. Box 2250, Haifa, 31021, Israel, and Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
| | - Ronnie Kosloff
- Chemical Research Support Unit, Department of Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel, Chemistry Department, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel, Rafael Intelligence and Security Directorate, P.O. Box 2250, Haifa, 31021, Israel, and Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem 91904, Israel
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Fisher M, Bar-Nes G, Zeiri Y, Sivan A. The effect of silica fume on biodegradation of cement paste and its capacity to immobilize strontium during exposure to microbial sulfur oxidation. Biodegradation 2007; 19:321-8. [PMID: 17578671 DOI: 10.1007/s10532-007-9138-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 06/02/2007] [Indexed: 10/23/2022]
Abstract
The disposal of low-level radioactive waste containing isotopes such as strontium by immobilization in cement paste has become common practice. However, the stability of cement paste in the environment may be impaired by sulfuric acid produced by sulfur-oxidizing bacteria. Since biodegradation rates in the environment of most radioactive waste burial sites are too low to be measured, determination of the degradation kinetics of cement paste is a difficult task. This study reports on the development of an accelerated biodegradation system for cement pastes in which the cement paste is exposed to a continuous culture of the sulfur-oxidizing bacterium Halothiobacillus neapolitanus. This system facilitated detection of the biodegradation processes in cement paste after as short a time as 15 days. A comparison of the durability of a cement paste blended with silica fume with that of unblended cement paste showed that the silica fume induced an increase in the leaching of Ca(+2) and Si and enhanced weight loss, indicating rapid deterioration in the structural integrity of the cement paste. The leaching of Sr(+2) from the silica fume amended cement paste was slightly reduced as compared with the non amended cement paste, indicating an increase in immobilization of strontium. Nevertheless, our findings do not support the use of silica fume as a suitable additive for immobilization of low-level radioactive waste.
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Affiliation(s)
- Merav Fisher
- Department of Biotechnology Engineering, Ben Gurion University of the Negev, P. O. Box 653, Beer Sheva 84100, Israel
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37
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Abstract
The dissociation of oxygen on a clean aluminum surface is studied theoretically. A nonadiabatic quantum dynamical model is used, based on four electronically distinct potential energy surfaces characterized by the extent of charge transfer from the metal to the adsorbate. A flat surface approximation is used to reduce the computation complexity. The conservation of the helicopter angular momentum allows Boltzmann averaging of the outcome of the propagation of a three degrees of freedom wave function. The dissociation event is simulated by solving the time-dependent Schrödinger equation for a period of 30 femtoseconds. As a function of incident kinetic energy, the dissociation yield follows the experimental trend. An attempt at simulation employing only the lowest adiabatic surface failed, qualitatively disagreeing with both experiment and nonadiabatic calculations. The final products, adsorptive dissociation and abstractive dissociation, are obtained by carrying out a semiclassical molecular dynamics simulation with surface hopping which describes the back charge transfer from an oxygen atom negative ion to the surface. The final adsorbed oxygen pair distribution compares well with experiment. By running the dynamical events backward in time, a correlation is established between the products and the initial conditions which lead to their production. Qualitative agreement is thus obtained with recent experiments that show suppression of abstraction by rotational excitation.
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Affiliation(s)
- Gil Katz
- Department of Physical Chemistry, the Hebrew University, Jerusalem 91904, Israel
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38
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Katz G, Zeiri Y, Kosloff R. Role of Vibrationally Excited NO in Promoting Electron Emission When Colliding with a Metal Surface: A Nonadiabatic Dynamic Model. J Phys Chem B 2005; 109:18876-80. [PMID: 16853429 DOI: 10.1021/jp052107k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A nonadiabatic quantum dynamic model has been developed to study the process of electron emission from a low-work-function metal surface. The process is initiated by scattering a highly vibrationally excited NO molecule from a surface composed of a Cs layer covering a Ru crystal. The model addresses the increasing quantum yield of the electron emission as a function of the molecular vibrational excitation and incident kinetic energy. The reaction mechanism is identified as a long-range harpooning electron transfer to a molecular ion which is then accelerated toward the surface. Upon impact, the molecular ion emits its excess electron.
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Affiliation(s)
- Gil Katz
- Department of Physical Chemistry and the Fritz Haber Research Center, the Hebrew University, Jerusalem 91904, Israel
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van Duin ACT, Zeiri Y, Dubnikova F, Kosloff R, Goddard WA. Atomistic-Scale Simulations of the Initial Chemical Events in the Thermal Initiation of Triacetonetriperoxide. J Am Chem Soc 2005; 127:11053-62. [PMID: 16076213 DOI: 10.1021/ja052067y] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To study the initial chemical events related to the detonation of triacetonetriperoxide (TATP), we have performed a series of molecular dynamics (MD) simulations. In these simulations we used the ReaxFF reactive force field, which we have extended to reproduce the quantum mechanics (QM)-derived relative energies of the reactants, products, intermediates, and transition states related to the TATP unimolecular decomposition. We find excellent agreement between the QM-predicted reaction products and those observed from 100 independent ReaxFF unimolecular MD cookoff simulations. Furthermore, the primary reaction products and average initiation temperature observed in these 100 independent unimolecular cookoff simulations match closely with those observed from a TATP condensed-phase cookoff simulation, indicating that unimolecular decomposition dominates the thermal initiation of the TATP condensed phase. Our simulations demonstrate that thermal initiation of condensed-phase TATP is entropy-driven (rather than enthalpy-driven), since the initial reaction (which mainly leads to the formation of acetone, O(2), and several unstable C(3)H(6)O(2) isomers) is almost energy-neutral. The O(2) generated in the initiation steps is subsequently utilized in exothermic secondary reactions, leading finally to formation of water and a wide range of small hydrocarbons, acids, aldehydes, ketones, ethers, and alcohols.
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Affiliation(s)
- Adri C T van Duin
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA.
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Zeiri Y. Foreword by the Guest Editors: Nonadiabatic Processes at Surfaces. Isr J Chem 2005. [DOI: 10.1002/ijch.5680450101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Dubnikova F, Kosloff R, Almog J, Zeiri Y, Boese R, Itzhaky H, Alt A, Keinan E. Decomposition of Triacetone Triperoxide Is an Entropic Explosion. J Am Chem Soc 2005; 127:1146-59. [PMID: 15669854 DOI: 10.1021/ja0464903] [Citation(s) in RCA: 217] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Both X-ray crystallography and electronic structure calculations using the cc-pVDZ basis set at the DFT B3LYP level were employed to study the explosive properties of triacetone triperoxide (TATP) and diacetone diperoxide (DADP). The thermal decomposition pathway of TATP was investigated by a series of calculations that identified transition states, intermediates, and the final products. Counterintuitively, these calculations predict that the explosion of TATP is not a thermochemically highly favored event. It rather involves entropy burst, which is the result of formation of one ozone and three acetone molecules from every molecule of TATP in the solid state.
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Affiliation(s)
- Faina Dubnikova
- Chemistry Department, Fritz Haber Institute for Molecular Dynamics, and Casali Institute of Applied Chemistry, Hebrew University, Jerusalem 91904, Israel
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Aviam O, Bar-Nes G, Zeiri Y, Sivan A. Accelerated biodegradation of cement by sulfur-oxidizing bacteria as a bioassay for evaluating immobilization of low-level radioactive waste. Appl Environ Microbiol 2004; 70:6031-6. [PMID: 15466547 PMCID: PMC522058 DOI: 10.1128/aem.70.10.6031-6036.2004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Disposal of low-level radioactive waste by immobilization in cement is being evaluated worldwide. The stability of cement in the environment may be impaired by sulfur-oxidizing bacteria that corrode the cement by producing sulfuric acid. Since this process is so slow that it is not possible to perform studies of the degradation kinetics and to test cement mixtures with increased durability, procedures that accelerate the biodegradation are required. Semicontinuous cultures of Halothiobacillus neapolitanus and Thiomonas intermedia containing thiosulfate as the sole energy source were employed to accelerate the biodegradation of cement samples. This resulted in a weight loss of up to 16% after 39 days, compared with a weight loss of 0.8% in noninoculated controls. Scanning electron microscopy of the degraded cement samples revealed deep cracks, which could be associated with the formation of low-density corrosion products in the interior of the cement. Accelerated biodegradation was also evident from the leaching rates of Ca(2+) and Si(2+), the major constituents of the cement matrix, and Ca exhibited the highest rate (up to 20 times greater than the control rate) due to the reaction between free lime and the biogenic sulfuric acid. Leaching of Sr(2+) and Cs(+), which were added to the cement to simulate immobilization of the corresponding radioisotopes, was also monitored. In contrast to the linear leaching kinetics of calcium, silicon, and strontium, the leaching pattern of cesium produced a saturation curve similar to the control curve. Presumably, the leaching of cesium is governed by the diffusion process, whereas the leaching kinetics of the other three ions seems to governed by dissolution of the cement.
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Affiliation(s)
- Orli Aviam
- Department of Biotechnology Engineering, Ben Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84100, Israel
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Jørgensen S, Dubnikova F, Kosloff R, Zeiri Y, Lilach Y, Asscher M. Theoretical Modeling of Steric Effect in Electron-Induced Desorption: CH3Br/O/Ru(001). J Phys Chem B 2004. [DOI: 10.1021/jp0477497] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | - Yehuda Zeiri
- Department of Chemistry, NRCN, P.O. Box 9001, Beer-Sheva 84190, Israel
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Affiliation(s)
- Micha Asscher
- Department of Physical Chemistry and Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Chemistry, Nuclear Research Center Negev, P.O.B. 9001, Beer-Sheva 84190, Israel
| | - Yehuda Zeiri
- Department of Physical Chemistry and Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Chemistry, Nuclear Research Center Negev, P.O.B. 9001, Beer-Sheva 84190, Israel
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Binetti M, Weiße O, Hasselbrink E, Katz G, Kosloff R, Zeiri Y. The role of nonadiabatic pathways and molecular rotations in the oxygen abstraction reaction on the Al(111) surface. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00586-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Dubnikova F, Kosloff R, Zeiri Y, Karpas Z. Novel Approach to the Detection of Triacetone Triperoxide (TATP): Its Structure and Its Complexes with Ions. J Phys Chem A 2002. [DOI: 10.1021/jp014189s] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Dubnikova
- Institute of Chemistry, Hebrew University, Jerusalem, Israel, Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem, Israel, and Chemistry Division, Nuclear Research Center, Negev, Beer-Sheva, Israel
| | - R. Kosloff
- Institute of Chemistry, Hebrew University, Jerusalem, Israel, Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem, Israel, and Chemistry Division, Nuclear Research Center, Negev, Beer-Sheva, Israel
| | - Y. Zeiri
- Institute of Chemistry, Hebrew University, Jerusalem, Israel, Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem, Israel, and Chemistry Division, Nuclear Research Center, Negev, Beer-Sheva, Israel
| | - Z. Karpas
- Institute of Chemistry, Hebrew University, Jerusalem, Israel, Fritz Haber Center for Molecular Dynamics, Hebrew University, Jerusalem, Israel, and Chemistry Division, Nuclear Research Center, Negev, Beer-Sheva, Israel
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Katz G, Yamashita K, Zeiri Y, Kosloff R. The Fourier method for tri-atomic systems in the search for the optimal coordinate system. J Chem Phys 2002. [DOI: 10.1063/1.1448285] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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