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Understanding chemical coupling in cyclic versus compact water clusters with the Ehrenfest Force. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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2
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Galvez Vallejo JL, Heredia JD, Gordon MS. Bonding analysis of water clusters using quasi-atomic orbitals. Phys Chem Chem Phys 2021; 23:18734-18743. [PMID: 34612411 DOI: 10.1039/d1cp02301b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The quasi-atomic orbital (QUAO) bonding analysis introduced by Ruedenberg and co-workers is used to develop an understanding of the hydrogen bonds in small water clusters, from the dimer through the hexamer (bag, boat, book, cyclic, prism and cage conformers). Using kinetic bond orders as a metric, it is demonstrated that as the number of waters in simple cyclic clusters increases, the hydrogen bonds strengthen, from the dimer through the cyclic hexamer. However, for the more complex hexamer isomers, the strength of the hydrogen bonds varies, depending on whether the cluster contains double acceptors and/or double donors. The QUAO analysis also reveals the three-center bonding nature of hydrogen bonds in water clusters.
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3
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Azizi A, Momen R, Kirk SR, Jenkins S. 3-D bond-paths of QTAIM and the stress tensor in neutral lithium clusters, Li m (m = 2-5), presented on the Ehrenfest force molecular graph. Phys Chem Chem Phys 2020; 22:864-877. [PMID: 31844863 DOI: 10.1039/c9cp05066c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this investigation we set out to understand the origins of non-nuclear attractors (NNAs) found for neutral lithium clusters Lim (m = 2-5) on the QTAIM molecular graph but not on the Ehrenfest force F(r) molecular graph. Therefore, we pursued the stress tensor σ(r) without using the dependency on the QTAIM partitioning, since previously σ(r) was only calculated within the QTAIM partitioning, to see if any indication of NNA character can be determined. Because the stress tensor σ(r) lacks an associated scalar- or vector-field as is the case for QTAIM and the Ehrenfest F(r) partitioning schemes respectively, a stress tensor σ(r) partitioning scheme cannot be constructed. Therefore, to overcome this difficulty we use next generation QTAIM, constructed from the most preferred directions of electronic charge density accumulation, to calculate the stress tensor σ(r) 3-D bond-paths on the Ehrenfest force F(r) molecular graph. Using next generation 3-D bond-paths within the Ehrenfest force F(r) partitioning, we can classify the degree of NNA character in the absence of NNAs. A much higher degree of NNA character is found to be present for the stress tensor σ(r) 3-D bond-paths than for the corresponding QTAIM or Ehrenfest force F(r) 3-D bond-paths. The stabilizing effect of the NNA is demonstrated by undertaking Li2 bond-path compression and stretching distortions sufficient to cause the annihilation of the NNA. The compression and stretching distortions also lead to a large increase in the 3-D bond-path asymmetry and persistent bond-path torsion respectively.
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Affiliation(s)
- Alireza Azizi
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource, National and Local Joint Engineering Laboratory for New Petro-chemical Materials and Fine Utilization of Resources, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.
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Azizi A, Momen R, Xu T, Kirk SR, Jenkins S. Non-nuclear attractors in small charged lithium clusters, Li mq (m = 2-5, q = ±1), with QTAIM and the Ehrenfest force partitioning. Phys Chem Chem Phys 2018; 20:24695-24707. [PMID: 30225484 DOI: 10.1039/c8cp05214j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this investigation we explore the function and existence of the non-nuclear attractor (NNA) for a series of small charged lithium clusters Limq (m = 2-5, q = ±1) using QTAIM and the Ehrenfest force F(r) partitioning schemes. The NNAs were found to be present in all of the Limq (m = 2-5, q = ±1) clusters for QTAIM, in contrast none were found for F(r). We discovered that the anionic and cationic lithium dimers are limiting cases for minimal and maximal impact of the NNA related to the relative sparseness of total charge density ρ(r) distributions respectively. Evidence is found that the NNA in the anionic dimer is in the process of being annihilated by two neighboring BCPs. We provide a measure of the size of the NNA and find for Limq (m = 2-5, q = ±1) that larger NNAs correlate with increased Li-Li separations. The NNA was determined to be a persistent feature by varying the Li separations for the cationic and anionic dimers. Very large Li separations failed to induce an NNA in the F(r) anionic dimer and therefore we conclude that F(r) is unable to detect NNAs. The metallicity ξ(rb) was also used to measure the sparseness of the distribution of ρ(r) and significant metallic character, on the basis of ξ(rb) > 1, was present for QTAIM but not for F(r), providing further evidence that F(r) cannot detect NNAs. Advantages of the use of Ehrenfest force F(r) partitioning scheme are discussed that include the design of nano-devices through tuning of the Ehrenfest potential VF(b) by the application of external forces such as a constant electric or strain field.
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Affiliation(s)
- Alireza Azizi
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.
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Li J, Xu T, Ping Y, van Mourik T, Früchtl H, Kirk SR, Jenkins S. Consequences of theory level choice evaluated with new tools from QTAIM and the stress tensor for a dipeptide conformer. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Momen R, Azizi A, Wang L, Ping Y, Xu T, Kirk SR, Li W, Manzhos S, Jenkins S. Exploration of the forbidden regions of the Ramachandran plot (ϕ-ψ) with QTAIM. Phys Chem Chem Phys 2018; 19:26423-26434. [PMID: 28944790 DOI: 10.1039/c7cp05124g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A new QTAIM interpretation of the Ramachandran plot is formulated from the most and least facile eigenvectors of the second-derivative matrix of the electron density with a set of 29 magainin-2 peptide conformers. The presence of QTAIM eigenvectors associated with the most and least preferred directions of electronic charge density explained the role of hydrogen bonding, HH contacts and the glycine amino acid monomer in peptide folding. The highest degree of occupation of the QTAIM interpreted Ramachandran plot was found for the glycine amino acid monomer compared with the remaining backbone peptide bonds. The mobility of the QTAIM eigenvectors of the glycine amino acid monomer was higher than for the other amino acids and was comparable to that of the hydrogen bonding, explaining the flexibility of the magainin-2 backbone. We experimented with a variety of hybrid QTAIM-Ramachandran plots to highlight and explain why the glycine amino acid monomer largely occupies the 'forbidden' region on the Ramachandran plot. In addition, the new hybrid QTAIM-Ramachandran plots contained recognizable regions that can be associated with concepts familiar from the conventional Ramachandran plot whilst retaining the character of the QTAIM most and least preferred regions.
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Affiliation(s)
- Roya Momen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.
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8
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Coa JC, Cardona-Galeano W, Restrepo A. Fe3+chelating quinoline–hydrazone hybrids with proven cytotoxicity, leishmanicidal, and trypanocidal activities. Phys Chem Chem Phys 2018; 20:20382-20390. [DOI: 10.1039/c8cp04174a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Neglected tropical diseases cause great concern in developing countries where there are millions of reported infected humans. Our calculations support a direct relationship between biological activity and the Fe3+chelating ability of the shown set of quinoline–hydrazone hybrids.
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Affiliation(s)
- Juan Carlos Coa
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
| | | | - Albeiro Restrepo
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
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Banach M, Konieczny L, Roterman I. Why do antifreeze proteins require a solenoid? Biochimie 2017; 144:74-84. [PMID: 29054801 DOI: 10.1016/j.biochi.2017.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
Abstract
Proteins whose presence prevents water from freezing in living organisms at temperatures below 0 °C are referred to as antifreeze proteins. This group includes molecules of varying size (from 30 to over 300 aa) and variable secondary/supersecondary conformation. Some of these proteins also contain peculiar structural motifs called solenoids. We have applied the fuzzy oil drop model in the analysis of four categories of antifreeze proteins: 1 - very small proteins, i.e. helical peptides (below 40 aa); 2 - small globular proteins (40-100 aa); 3 - large globular proteins (>100 aa) and 4 - proteins containing solenoids. The FOD model suggests a mechanism by which antifreeze proteins prevent freezing. In accordance with this theory, the presence of the protein itself produces an ordering of water molecules which counteracts the formation of ice crystals. This conclusion is supported by analysis of the ordering of hydrophobic and hydrophilic residues in antifreeze proteins, revealing significant variability - from perfect adherence to the fuzzy oil drop model through structures which lack a clearly defined hydrophobic core, all the way to linear arrangement of alternating local minima and maxima propagating along the principal axis of the solenoid (much like in amyloids). The presented model - alternative with respect to the ice docking model - explains the antifreeze properties of compounds such as saccharides and fatty acids. The fuzzy oil drop model also enables differentiation between amyloids and antifreeze proteins.
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Affiliation(s)
- M Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Lazarza 16, 31-530, Krakow, Poland
| | - L Konieczny
- Chair of Medical Biochemistry, Jagiellonian University, Medical College, Kopernika 7, 31-034, Krakow, Poland
| | - I Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Lazarza 16, 31-530, Krakow, Poland.
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Farfán P, Echeverri A, Diaz E, Tapia JD, Gómez S, Restrepo A. Dimers of formic acid: Structures, stability, and double proton transfer. J Chem Phys 2017; 147:044312. [DOI: 10.1063/1.4985880] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Paola Farfán
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52–21, Medellín, Colombia
| | - Andrea Echeverri
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52–21, Medellín, Colombia
| | - Estefanía Diaz
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52–21, Medellín, Colombia
| | - Juan David Tapia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52–21, Medellín, Colombia
| | - Sara Gómez
- Departamento de Educación y Ciencias Básicas, Instituto Tecnológico Metropolitano, Calle 73 No. 76A–354, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52–21, Medellín, Colombia
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11
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Dissecting the role of dispersion on the quantum topology phase diagram of monosaccharide isomers. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-016-1869-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Wang L, Huan G, Momen R, Azizi A, Xu T, Kirk SR, Filatov M, Jenkins S. QTAIM and Stress Tensor Characterization of Intramolecular Interactions Along Dynamics Trajectories of a Light-Driven Rotary Molecular Motor. J Phys Chem A 2017; 121:4778-4792. [PMID: 28586210 DOI: 10.1021/acs.jpca.7b02347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A quantum theory of atoms in molecules (QTAIM) and stress tensor analysis was applied to analyze intramolecular interactions influencing the photoisomerization dynamics of a light-driven rotary molecular motor. For selected nonadiabatic molecular dynamics trajectories characterized by markedly different S1 state lifetimes, the electron densities were obtained using the ensemble density functional theory method. The analysis revealed that torsional motion of the molecular motor blades from the Franck-Condon point to the S1 energy minimum and the S1/S0 conical intersection is controlled by two factors: greater numbers of intramolecular bonds before the hop-time and unusually strongly coupled bonds between the atoms of the rotor and the stator blades. This results in the effective stalling of the progress along the torsional path for an extended period of time. This finding suggests a possibility of chemical tuning of the speed of photoisomerization of molecular motors and related molecular switches by reshaping their molecular backbones to decrease or increase the degree of coupling and numbers of intramolecular bond critical points as revealed by the QTAIM/stress tensor analysis of the electron density. Additionally, the stress tensor scalar and vector analysis was found to provide new methods to follow the trajectories, and from this, new insight was gained into the behavior of the S1 state in the vicinity of the conical intersection.
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Affiliation(s)
- Lingling Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
| | - Guo Huan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
| | - Roya Momen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
| | - Alireza Azizi
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
| | - Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
| | - Steven R Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
| | - Michael Filatov
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha, Hunan 410081, China
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Xu T, Farrell J, Momen R, Azizi A, Kirk SR, Jenkins S, Wales DJ. A stress tensor eigenvector projection space for the (H2O)5 potential energy surface. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2016.11.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Hu MX, Xu T, Momen R, Huan G, Kirk SR, Jenkins S, Filatov M. A QTAIM and stress tensor investigation of the torsion path of a light-driven fluorene molecular rotary motor. J Comput Chem 2016; 37:2588-96. [PMID: 27671359 DOI: 10.1002/jcc.24487] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/21/2016] [Accepted: 08/23/2016] [Indexed: 11/10/2022]
Abstract
The utility of the QTAIM/stress tensor analysis method for characterizing the photoisomerization of light driven molecular rotary machines is investigated on the example of the torsion path in fluorene molecular motor. The scalar and vector descriptors of QTAIM/stress tensor reveal additional information on the bonding interactions between the rotating units of the motor, which cannot be obtained from the analysis of the ground and excited state potential energy surfaces. The topological features of the fluorene motor molecular graph display that, upon the photoexcitation a certain increase in the torsional stiffness of the rotating bond can be attributed to the increasing topological stability of the rotor carbon atom attached to the rotation axle. The established variations in the torsional stiffness of the rotating bond may cause transfer of certain fraction of the torsional energy to other internal degrees of freedom, such as the pyramidalization distortion. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ming Xing Hu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China.,Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Tianlv Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China.,Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Roya Momen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China.,Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Guo Huan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China.,Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Steven R Kirk
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China.,Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Samantha Jenkins
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China.,Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Michael Filatov
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Korea
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Xu T, Farrell J, Xu Y, Momen R, Kirk SR, Jenkins S, Wales DJ. QTAIM and stress tensor interpretation of the (H2
O)5
potential energy surface. J Comput Chem 2016; 37:2712-2721. [DOI: 10.1002/jcc.24498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Tianlv Xu
- College of Chemistry & Chemical Engineering, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE; College of Chemistry and Chemical Engineering, Hunan Normal University; Changsha Hunan 410081 China
| | - James Farrell
- Department of Chemistry, Lensfield Road; Cambridge University; UK
| | - Yuning Xu
- College of Chemistry & Chemical Engineering, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE; College of Chemistry and Chemical Engineering, Hunan Normal University; Changsha Hunan 410081 China
| | - Roya Momen
- College of Chemistry & Chemical Engineering, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE; College of Chemistry and Chemical Engineering, Hunan Normal University; Changsha Hunan 410081 China
| | - Steven R. Kirk
- College of Chemistry & Chemical Engineering, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE; College of Chemistry and Chemical Engineering, Hunan Normal University; Changsha Hunan 410081 China
| | - Samantha Jenkins
- College of Chemistry & Chemical Engineering, Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province of MOE; College of Chemistry and Chemical Engineering, Hunan Normal University; Changsha Hunan 410081 China
| | - David J. Wales
- Department of Chemistry, Lensfield Road; Cambridge University; UK
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16
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A QTAIM exploration of the competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Zapata-Escobar AD, Cárcamo-Camacho T, Hadad CZ, Restrepo A. On the nature of the trimer, tetramer, and pentamer of ammonia borane. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1853-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Flórez E, Maldonado AF, Aucar GA, David J, Restrepo A. Microsolvation of methylmercury: structures, energies, bonding and NMR constants (199Hg,13C and17O). Phys Chem Chem Phys 2016; 18:1537-50. [DOI: 10.1039/c5cp04826e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hartree–Fock (HF) and second order perturbation theory (MP2) calculations within the scalar and full relativistic frames were carried out in order to determine the equilibrium geometries and interaction energies between cationic methylmercury (CH3Hg+) and up to three water molecules.
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Affiliation(s)
- Edison Flórez
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
| | - Alejandro F. Maldonado
- Physics Department
- Natural and Exact Science Faculty
- Northeastern University of Argentina and Institute of Modelling and Innovation on Technology
- IMIT
- Corrientes
| | - Gustavo A. Aucar
- Physics Department
- Natural and Exact Science Faculty
- Northeastern University of Argentina and Institute of Modelling and Innovation on Technology
- IMIT
- Corrientes
| | - Jorge David
- Departamento de Ciencias Físicas
- Universidad EAFIT
- Medellín
- Colombia
| | - Albeiro Restrepo
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
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Hadad CZ, Jenkins S, Flórez E. Unusual solvation through both p-orbital lobes of a carbene carbon. J Chem Phys 2015; 142:094302. [DOI: 10.1063/1.4913568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- C. Z. Hadad
- Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, A. A. 1226 Medellín, Colombia
| | - Samantha Jenkins
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Elizabeth Flórez
- Departamento de Ciencias Básicas, Universidad de Medellín, Carrera 87 N° 30-65, Medellín, Colombia
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20
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Varadwaj PR, Varadwaj A, Jin BY. Unusual bonding modes of perfluorobenzene in its polymeric (dimeric, trimeric and tetrameric) forms: entirely negative fluorine interacting cooperatively with entirely negative fluorine. Phys Chem Chem Phys 2015; 17:31624-45. [DOI: 10.1039/c5cp03209a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Laplacian of the charge density plot for the tetramer of perfluorobenzene, displaying the attraction between entirely negative fluorine atoms, as well as the windmill type intermolecular topology between those atoms.
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Affiliation(s)
| | - Arpita Varadwaj
- Department of Chemistry
- National Taiwan University
- Taipei
- Republic of China
| | - Bih-Yaw Jin
- Department of Chemistry
- National Taiwan University
- Taipei
- Republic of China
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21
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Kumar A, Gadre SR, Chenxia X, Tianlv X, Kirk SR, Jenkins S. Hybrid QTAIM and electrostatic potential-based quantum topology phase diagrams for water clusters. Phys Chem Chem Phys 2015; 17:15258-73. [DOI: 10.1039/c5cp01039j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The topological diversity of sets of isomers of water clusters (W = H2O)n, 7 ≤ n ≤ 10, is analyzed employing the scalar fields of total electronic charge density ρ(r) and the molecular electrostatic potential (MESP).
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Affiliation(s)
- Anmol Kumar
- Department of Chemistry
- Indian Institute of Technology
- Kanpur 208016
- India
| | - Shridhar R. Gadre
- Department of Chemistry
- Indian Institute of Technology
- Kanpur 208016
- India
| | - Xiao Chenxia
- National and Local United Engineering Laboratory for New Petrochemical Materials and Fine Utilization of Resources
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China)
- Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province
- College of Chemistry and Chemical Engineering
- Hunan Normal University
| | - Xu Tianlv
- National and Local United Engineering Laboratory for New Petrochemical Materials and Fine Utilization of Resources
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China)
- Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province
- College of Chemistry and Chemical Engineering
- Hunan Normal University
| | - Steven Robert Kirk
- National and Local United Engineering Laboratory for New Petrochemical Materials and Fine Utilization of Resources
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China)
- Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province
- College of Chemistry and Chemical Engineering
- Hunan Normal University
| | - Samantha Jenkins
- National and Local United Engineering Laboratory for New Petrochemical Materials and Fine Utilization of Resources
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China)
- Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province
- College of Chemistry and Chemical Engineering
- Hunan Normal University
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22
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Timm MJ, Matta CF, Massa L, Huang L. The Localization–Delocalization Matrix and the Electron-Density-Weighted Connectivity Matrix of a Finite Graphene Nanoribbon Reconstructed from Kernel Fragments. J Phys Chem A 2014; 118:11304-16. [DOI: 10.1021/jp508490p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew J. Timm
- Department
of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M2J6, Canada
| | - Chérif F. Matta
- Department
of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M2J6, Canada
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H4J3, Canada
- Department
of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H3C3, Canada
| | - Lou Massa
- Hunter
College and the Graduate School, City University of New York, New York, New York 10065, United States
| | - Lulu Huang
- Center
for Computational Materials Science, Naval Research Laboratory, Washington, D.C. 20375-5341, United States
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23
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Ibargüen C, Guerra D, Hadad CZ, Restrepo A. Very weak interactions: structures, energies and bonding in the tetramers and pentamers of hydrogen sulfide. RSC Adv 2014. [DOI: 10.1039/c4ra09430a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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Xiao CX, Xu T, Maza JR, Figueredo FA, Kirk SR, Jenkins S. A QTAIM perspective of the Si6Li6 potential energy surface using quantum topology phase diagrams. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.06.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Xu T, Jenkins S, Xiao CX, Maza JR, Kirk SR. The Pt site reactivity of the molecular graphs of Au6Pt isomers. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.10.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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27
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Albrecht L, Chowdhury S, Boyd RJ. Hydrogen Bond Cooperativity in Water Hexamers: Atomic Energy Perspective of Local Stabilities. J Phys Chem A 2013; 117:10790-9. [DOI: 10.1021/jp407371c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Albrecht
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Saptarshi Chowdhury
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Russell J. Boyd
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
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28
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Polestshuk PM. Ad hoc methods for accurate determination of Bader's atomic boundary. J Chem Phys 2013; 139:054108. [DOI: 10.1063/1.4816933] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Acelas N, Hincapié G, Guerra D, David J, Restrepo A. Structures, energies, and bonding in the water heptamer. J Chem Phys 2013; 139:044310. [DOI: 10.1063/1.4816371] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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30
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Structural characterization of the (MeSH)4 potential energy surface. J Mol Model 2013; 19:2173-81. [DOI: 10.1007/s00894-013-1765-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 01/10/2013] [Indexed: 10/27/2022]
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31
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Acelas NY, Mejia SM, Mondragón F, Flórez E. Density functional theory characterization of phosphate and sulfate adsorption on Fe-(hydr)oxide: Reactivity, pH effect, estimation of Gibbs free energies, and topological analysis of hydrogen bonds. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Microsolvation of Mg2+, Ca2+: strong influence of formal charges in hydrogen bond networks. J Mol Model 2013; 19:1763-77. [DOI: 10.1007/s00894-012-1716-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
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33
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Ibargüen C, Manrique-Moreno M, Hadad CZ, David J, Restrepo A. Microsolvation of dimethylphosphate: a molecular model for the interaction of cell membranes with water. Phys Chem Chem Phys 2013; 15:3203-11. [DOI: 10.1039/c2cp42778h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Maza JR, Jenkins S, Kirk SR, Anderson JSM, Ayers PW. The Ehrenfest force topology: a physically intuitive approach for analyzing chemical interactions. Phys Chem Chem Phys 2013; 15:17823-36. [DOI: 10.1039/c3cp52687a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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35
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Sánchez-Lozano M, Cabaleiro-Lago EM, Hermida-Ramón JM, Estévez CM. A computational study of the protonation of simple amines in water clusters. Phys Chem Chem Phys 2013; 15:18204-16. [DOI: 10.1039/c3cp51668g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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36
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Jenkins S, Kirk SR, Rong C, Yin D. The cis-effect using the topology of the electronic charge density. Mol Phys 2012. [DOI: 10.1080/00268976.2012.745631] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Samantha Jenkins
- a Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province , College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha Hunan 410081 , China
| | - Steven R. Kirk
- a Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province , College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha Hunan 410081 , China
| | - Chunying Rong
- a Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province , College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha Hunan 410081 , China
| | - Dulin Yin
- a Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province , College of Chemistry and Chemical Engineering, Hunan Normal University , Changsha Hunan 410081 , China
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37
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Chopra D. Advances in understanding of chemical bonding: inputs from experimental and theoretical charge density analysis. J Phys Chem A 2012; 116:9791-801. [PMID: 22928665 DOI: 10.1021/jp306169f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of charge density analysis has undergone a major renaissance in the last two decades. In recent years, the characterization of bonding features associated with atoms in molecules and in crystals has been explored using high-resolution X-ray diffraction data (laboratory or synchrotron) complemented by high level ab initio theoretical calculations. The extraction of one electron topological properties, namely, electrostatic charges, dipole moment and higher moments, electrostatic potential, electric field gradients, in addition to evaluation of the local kinetic and potential energy densities, have contributed toward an understanding of the electron density distributions in molecular solids. New topological descriptors, namely, the source function (SF) and electron localization function (ELF) provide additional information as regards characterization of the topology of the electron density. In addition, delocalization indices have also been developed to account for bonding features pertinent to M-M bonds. The evaluation of these properties have contributed significantly toward the understanding of intra- and intermolecular bonding features in organic, inorganic, and biomolecules in the crystalline phase, with concomitant applications in the understanding of chemical reactivity and material/biological properties. In recent years, the focus has strongly shifted toward the understanding of structure-property relationships in organometallic complexes containing labile M-C bonds in the crystal structure with subsequent implications in catalysis. This perspective aims to highlight the major developments in electron density measurements in the past few years and provides pointers directed toward the potential use of this technique in future applications for an improved understanding of chemical bonding in systems that have been unexplored.
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Affiliation(s)
- Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462023, India.
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38
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Yepes D, Kirk SR, Jenkins S, Restrepo A. Structures, energies and bonding in neutral and charged Li microclusters. J Mol Model 2012; 18:4171-89. [DOI: 10.1007/s00894-012-1406-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 03/08/2012] [Indexed: 11/24/2022]
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