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The shape effect and its consequences for polar surfaces and for heterogeneous catalysis. Phys Chem Chem Phys 2023; 25:13308-13319. [PMID: 37133928 DOI: 10.1039/d3cp00996c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In this paper we develop the shape effect, which is relevant for crystalline materials whose size is larger than that of the thermodynamic limit. According to this effect the electronic properties of one surface of a crystal depend upon all of its surfaces, i.e. on the overall shape. At first, qualitative mathematical arguments are presented for the existence of this effect based on the conditions for the stability of polar surfaces. Our treatment explains why such surfaces are observed even though earlier theory indicated that they should not exist. Then, models are developed from which it is found computationally that changing the shape of a polar crystal can substantially alter the magnitude of its surface charges. Apart from surface charges, it follows that the crystal shape will also significantly affect bulk properties, most notably polarization and piezoelectric responses. Additional model calculations show a strong shape effect on the activation energy for heterogeneous catalysis primarily through local surface charges rather than a non-local/long range electrostatic potential.
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2
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Properties of Naked Silver Clusters with Up to 100 Atoms as Found with Embedded-Atom and Density-Functional Calculations. Molecules 2023; 28:molecules28073266. [PMID: 37050029 PMCID: PMC10096883 DOI: 10.3390/molecules28073266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
The structural and energetic properties of small silver clusters Agn with n = 2-100 atoms are reported. For n = 2-100 the embedded atom model for the calculation of the total energy of a given structure in combination with the basin-hopping search strategy for an unbiased structure optimization has been used to identify the energies and structures of the three energetically lowest-lying isomers. These optimized structures for n = 2-11 were subsequently studied further through density-functional-theory calculations. These calculations provide additional information on the electronic properties of the clusters that is lacking in the embedded-atom calculations. Thereby, also quantities related to the catalytic performance of the clusters are studied. The calculated properties in comparison to other available theoretical and experimental data show a good agreement. Previously unidentified magic (i.e., particularly stable) clusters have been found for n>80. In order to obtain a more detailed understanding of the structural properties of the clusters, various descriptors are used. Thereby, the silver clusters are compared to other noble metals and show some similarities to both copper and nickel systems, and also growth patterns have been identified. All vibrational frequencies of all the clusters have been calculated for the first time, and here we focus on the highest and lowest frequencies. Structural effects on the calculated frequencies were considered.
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3
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Mechanistic insights into aerobic oxidative cleavage of glycol catalyzed by an Anderson-type polyoxometalate [IMo 6O 24] 5. J Mol Model 2023; 29:57. [PMID: 36710274 DOI: 10.1007/s00894-023-05458-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/17/2023] [Indexed: 01/31/2023]
Abstract
A computational investigation of the aerobic oxidative C-C bond cleavage reaction of glycol catalyzed by an Anderson-type heteropolyanion HPA [IMo6O24]5- in the presence of acetonitrile as solvent has been performed at the WB97XD/6-31G(d,p)/lanl2dz level. Two reaction pathways have been identified. The catalytic cycle of each pathway consists of three steps: oxidation cleavage of a glycol molecule by the HPA, oxidation of the HPA by one dioxygen molecule, and, finally, oxidation of a second glycol and regeneration of the catalyst. These reaction pathways have been thoroughly investigated in terms of energetic, natural bond orbital (NBO), natural charges, and geometrical parameters. It is found that (i) even though the top oxygen atoms of the Anderson heteropolyanion are not the most negatively charged ones, they are more likely to react with the diol hydroxyl groups, (ii) a direct relationship between the presence of the iodine ion I(VII) and the studied oxidation reaction could not be identified, and (iii) in terms of energy, the transfer of the two hydrogen atoms is the most energetic step.
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4
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Theoretical Study on Non-Linear Optics Properties of Polycyclic Aromatic Hydrocarbons and the Effect of Their Intercalation with Carbon Nanotubes. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010110. [PMID: 36615304 PMCID: PMC9822052 DOI: 10.3390/molecules28010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Results of a theoretical study devoted to comparing NLO (non-linear optics) responses of derivatives of tetracene, isochrysene, and pyrene are reported. The static hyperpolarizability β, the dipole moment μ, the HOMO and LUMO orbitals, and their energy gap were calculated using the CAM-B3LYP density functional combined with the cc-pVDZ basis set. The para-disubstituted NO2-tetracene-N(CH3)2 has the highest NLO response, which is related to a large intramolecular charge transfer. Adding vinyl groups to the para-disubstituted NO2-tetracene-N(CH3)2 results in an increase in the NLO responses. We further investigated the effect of the intercalation of various push-pull molecules inside an armchair single-walled carbon nanotube. The intercalation leads to increased NLO responses, something that depends critically on the position of the guest molecule and/or on functionalization of the nanotube by donor and attractor groups.
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5
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Nonlinear optical properties DFT calculations of polyacethylene and copolymers models substituted with aldimines chromophores as side chains. J Comput Chem 2022; 43:1701-1718. [PMID: 35938777 DOI: 10.1002/jcc.26971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 11/05/2022]
Abstract
Aldimine derivatives chromophores grafted on polyacetylene oligomers were first designed to investigate the nonlinear optical (NLO) response of the resulting materials using CAMB3LYP method. The effects of different factors such as the chain length separating the substitutions as well as the configurations and the orientations of these latter, were examined and discussed. In a second part of this paper, NLO responses, in particular the static hyperpolarizabilities of polyvinyl oligomers substituted by aldimine chromophores via carboxylic groups and by pyrrolidone groups were calculated for different configurations. The stability and the hydrogen bonding in each oligomer were also discussed.
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6
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DFT evaluation of structural, electronic and variation properties for complex carbohydrates with biological interest. J Biomol Struct Dyn 2022:1-9. [PMID: 35838154 DOI: 10.1080/07391102.2022.2099975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The synthetic bicyclic bis(hemiacetals) compounds 1,5-pyranose-9,7-pyranoses, with a structural analogy to the bicyclic monosaccharide Bradyrhizose, have been described here based on a theoretical approach, using DFT calculations with the B3LYP functional combined with the 6-311 + G(d,p) basis set. First, we have performed a geometrical and electronic properties description of (1 R,9S), (1S,9S) and (1S,9R)-1,5-pyranose-9,7-pyranoses. Results analysis indicated that, slight differences in the three-dimensional orientations of their atoms lead to an enormous difference in chemical reactivity. Consequently, (1S,9S) and (1S,9R) isomers are predicted to be the most resembling the natural bradyrhizose in structural features. To enhance the performance of these two isomers, a set of modifications through functional groups attached to the reactive sites were determined by local reactivity descriptors. Subsequently, in order to get more information on the obtained derivatives for both isomers, HOMO, LUMO, Egap and four electronic parameters were calculated and compared. The substituted systems show a good performance in chemical reactivity than the unmodified parent compounds.Communicated by Ramaswamy H. Sarma.
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Efficient model photosensitizers based on metallocenyl complexes with thiophene-N = N-pyrimidine as π-conjugated bridge and cyanoacrylate as an anchoring group: a density functional theory study. J Mol Model 2022; 28:213. [PMID: 35799032 DOI: 10.1007/s00894-022-05208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/26/2022] [Indexed: 11/28/2022]
Abstract
Eight push-pull systems involving containing four transition metals (iron, ruthenium, cobalt, and nickel), metallocenes as donor groups, cyanoacrylate as electron attractor group, and thiophene-N = N- pyrimidine derivatives as π-conjugated bridges were designed and studied using DFT and TD-DFT methods involving B3LYP and CAM-B3LYP functionals combined with the cc-pVDZ/LANL2DZ basis sets. The main purpose of this work is to determine the effect of metallocene in improving the photosensitization property of such chromophores. This was done by calculating their light-harvesting efficiency LHE as well as other properties employed for DSSC application. The considered dyes were first studied in the gas phase, then in the presence of TiO2 nanoparticles representing the semi-conductor, and finally in the presence of a specific implicit solvent. The presence of iron as metal involved in the metallocene group supplemented by extending the π-conjugated bridge by a cyanovinyl spacer was demonstrated so as to give the most optimal response taking into account the lower cost and toxicity as well as the friendliness to the environment of iron as metal.
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Role of the Backbone when Optimizing Functional Groups─A Theoretical Study Based on an Improved Inverse-Design Approach. J Phys Chem A 2022; 126:1289-1299. [PMID: 35166555 DOI: 10.1021/acs.jpca.1c10437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present an improved inverse-design approach for automatically identifying molecular (or other) systems with optimal values for prechosen properties. The new approach uses SMILES (simplified molecular input line entry system) to describe molecular structures efficiently, a genetic algorithm to optimize the molecules automatically, and the DFTB+ (self-consistent charge density functional tight-binding) method to calculate electronic properties. Thereby, almost every class of materials─even macromolecules or monomers─can be studied easily. Without crossover operators but with only mutation operators, the genetic algorithm is more adaptive to SMILES while keeping its efficiency. DFTB+ is more accurate than the DFTB method used in our previous inverse-design approach for the study of excited states and charge transfer processes. The improved approach is applied to optimize benzene, pyridine, pyridazine, pyrimidine, and pyrazine derivatives for seven electronic properties, which all are highly relevant and important for the performance of molecules in solar cells. We found that for some electronic properties, the precise composition and structure of the backbone have remarkable impacts on the value of the electronic properties and/or on the set of functional groups that leads to the best performance. On the contrary, for other properties, these effects are less pronounced. The reasonable optimal functional groups and/or substitution patterns are reported.
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Abstract
AbstractUsing a combination of genetic algorithms for the unbiased structure optimization and a Gupta many-body potential for the calculation of the energetic properties of a given structure, we determine the putative total-energy minima for all $$\hbox {Ag}_{m} \hbox {Rh}_n$$
Ag
m
Rh
n
clusters with a total number of atoms $$m+n$$
m
+
n
up to 55. Subsequently, we use various descriptors to analyze the obtained structural and energetic properties. With the help of a similarity function, we show that the pure Ag and Rh clusters are structurally similar for sizes up to around 20 atoms. The same approach gives that the mixed clusters tend to possess a larger structural similarity with the pure Rh clusters than with the pure Ag clusters. However, for clusters with $$m\simeq n\ge 25$$
m
≃
n
≥
25
, other structures dominate. The effective coordination numbers for the Ag and Rh atoms as well as the radial distributions of those atoms indicate that there is a tendency towards segregation with Rh atoms forming an inner part and the Ag atoms forming a shell. Only few clusters, all with a fairly large total number of atoms, are found to be particularly stable.
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Expression of concern on: M. Emin Cinar, Thermal reaction of 1,8-diketone: A computational study, Computational and theoretical Chemistry 1170 (2019) 112641, https://doi.org/10.1016/j.comptc.2019.112641. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2020.113000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Theoretical study of the structural and energetic properties of platinum clusters with up to 60 atoms. Struct Chem 2020. [DOI: 10.1007/s11224-020-01679-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Mechanistic Details and Conformational Behavior of Selective Peptide Linkage Facilitated by Au nClusters. ChemistrySelect 2020. [DOI: 10.1002/slct.202001564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Optimizing small conjugated molecules for solar-cell applications using an inverse-design method. J Mol Graph Model 2020; 100:107654. [PMID: 32682307 DOI: 10.1016/j.jmgm.2020.107654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 10/23/2022]
Abstract
Small organic conjugated molecules are key elements for low-cost photovoltaic devices. One example is cyanopyridone molecules. By modifying these molecules, for instance through optimally chosen functional groups attached to the backbone, their properties can be improved. However, the very large number of possible modifications makes it difficult to identify the best performing molecules. In the present work, we have used a computational inverse-design approach (PooMa) to identify the positions and types of functional groups attached to a modified cyanopyridone that lead to the best performance in solar-energy harvesting. A QSPR model based on five electronic descriptors has been used to determine the properties of solar cells. Our approach uses a genetic algorithm to search the chemical space containing 184 (104,976) substituted cyanopyridone systems and predicts out of those the best 20 molecules with optimal performance efficiencies (PCE). PooMa uses the Density-Functional Tight-Binding (DFTB) method for calculating the electronic properties. DFTB is a fast method with acceptable accuracy and, therefore, can be used on a normal desktop without expensive hard- or software. In order to get further information about our suggested systems, a DFT method and its derivative TD-DFT are applied.
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Theoretical study of the mechanism behind the site- and enantio-selectivity of C-H functionalization catalysed by chiral dirhodium catalyst. Phys Chem Chem Phys 2020; 22:9561-9572. [PMID: 32319983 DOI: 10.1039/d0cp00249f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C-H functionalization is very important for the synthesis of pharmaceuticals and complex natural products. Rhodium carbenoids, obtained when a dirhodium(ii) catalyst containing a crown formed by chiral ligands reacts with diazo compounds with both an electron donating group and an electron withdrawing group, play an important part in controlling site- and enantio-selectivity for functionalization of non-activated C-H bonds. It has earlier been demonstrated that the tertiary C-H bond is more favored to be functionalized inside the crown of the dirhodium catalyst with S-configuration ligands compared with the secondary and primary C-H bonds although the latter possess weaker steric effects. We argue that the higher site- and enantio-selectivity for some types of C-H bond functionalization can be related to intermolecular hydrogen bonding, steric hindrance, and weak interactions when the dirhodium catalyst is interacting with the chiral ligands.
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15
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Competition between tubular, planar and cage geometries: a complete picture of structural evolution of Bn (n = 31–50) clusters. Phys Chem Chem Phys 2020; 22:12959-12966. [DOI: 10.1039/d0cp01256d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Stimulated by the early theoretical prediction of B80 fullerene and the experimental finding of the B40 cage, the structures of medium-sized boron clusters have attracted intensive research interest during the last decade, but a complete picture of their size-dependent structural evolution remains a puzzle.
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Ultranarrow heterojunctions of armchair-graphene nanoribbons as resonant-tunnelling devices. Phys Chem Chem Phys 2019; 21:24867-24875. [PMID: 31517350 DOI: 10.1039/c9cp04368c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A systematic investigation is performed on the electronic transport properties of armchair-graphene nanoribbon (AGNR) heterojunctions using spin-polarized density functional theory calculations in combination with the non-equilibrium Green's function formalism. 9-AGNR and 5-AGNR structures are used to form a single-well configuration by sandwiching a 5-AGNR between two 9-AGNRs. At the same time, these 9-AGNRs are matched at the left and right to electrodes, 9 and 5 being the number of carbon dimers as width. This heterojunction mimics an electronic device with two potential barriers (9-AGNR) and one quantum well (5-AGNR) where quasi-bound states are confined. First, we study the ground state properties, and then we calculate the electron transport properties of this device as a function of the well width. We show the presence of electronic tunnelling resonances between the barriers by delocalized electron density inside the well's structure. This is corroborated by transmission curves, localized densities of states (LDOS), current-vs.-bias voltage results, and the trend of the resonances as a function of the well width. This work shows that carbon AGNRs may be used as resonant-tunnelling devices for applications in nanoelectronics.
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Density Functional Theory Descriptors for Ionic Liquids and the Introduction of a Coulomb Correction. J Phys Chem A 2019; 123:4188-4200. [DOI: 10.1021/acs.jpca.9b01831] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Abstract
The canonical thermodynamics of clusters is determined quantum mechanically in the general case of multiple minima of the potential energy surface (PES) using the superposition approximation. As an illustration of the consequences of our approach, we study in detail the thermodynamic properties of CuN clusters with N from 2 to 150 as a function of cluster size, temperature, and number of isomers. Thereby, for instance, solid-solid transition temperatures for several cluster sizes are determined. We show that the cluster vibrations have a strong impact on the stability of the clusters and that this can be observed not only at medium and high temperatures but also at low temperatures and even at T = 0 K. Thus, including zero-point corrections can change the relative energetic ordering of different isomers. This isomeric effect results in an oscillatory dependence of the heat capacity on cluster size at moderate and high temperatures. Moreover, for the identification of magic clusters at non-vanishing temperature, the Helmholtz free energy is analyzed as a function of cluster size and temperature within a one-, two-, and three-minima model of the PES. Thereby, we demonstrate that the concept of magic clusters is strongly temperature dependent so that in several cases clusters change from being magic or non-magic at T = 0 K to be the opposite at non-vanishing temperature. We emphasize that all these effects are not specific for copper clusters alone but can also be observed in other metal or semiconductor nanoclusters.
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Application of an inverse-design method to optimizing porphyrins in dye-sensitized solar cells. Phys Chem Chem Phys 2019; 21:5834-5844. [PMID: 30806399 DOI: 10.1039/c8cp07722c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dye-sensitized solar cells (DSSCs) have attracted much interest during the past few decades. However, it is still a tremendous challenge to identify organic molecules that give an optimal power conversion efficiency (PCE). Here, we apply our recently developed, inverse-design method for this issue with the special aim of identifying porphyrins with promisingly high PCE. It turns out that the calculations lead to the prediction of 15 new molecules with optimal performances and for which none so far has been studied. These porphyrin derivatives will in the near future be synthesized and subsequently tested experimentally. Our inverse-design approach, PooMa, is based on the strategy of providing suggestions for molecular systems with optimal properties. PooMa has been developed as a tool that requires minimal resources and, therefore, builds on various approximate methods. It uses genetic algorithm to screen thousands (or often more) of molecules. For each molecule, the density-functional tight-binding (DFTB) method is used for calculating the electronic properties. In the present work, five different electronic properties are determined, all of which are related to optical performance. Subsequently, a quantitative structure-property relationship (QSPR) model is constructed that can predict the PCE through those five electronic properties. Finally, we benchmark our results through more accurate DFT calculations that give further information on the predicted optimal molecules.
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Density Functional Theory Descriptors for Ionic Liquids and the Charge-Transfer Interpretation of the Haven Ratio. J Phys Chem A 2019; 123:851-861. [DOI: 10.1021/acs.jpca.8b10827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Theoretical Treatment for Properties of Surfaces and Their Interplay with Bulk Properties of Crystals. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Electronic orbital response of regular extended and infinite periodic systems to magnetic fields. I. Theoretical foundations for static case. J Chem Phys 2018; 147:104101. [PMID: 28915743 DOI: 10.1063/1.5001261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theoretical treatment for the orbital response of an infinite, periodic system to a static, homogeneous, magnetic field is presented. It is assumed that the system of interest has an energy gap separating occupied and unoccupied orbitals and a zero Chern number. In contrast to earlier studies, we do not utilize a perturbation expansion, although we do assume the field is sufficiently weak that the occurrence of Landau levels can be ignored. The theory is developed by analyzing results for large, finite systems and also by comparing with the analogous treatment of an electrostatic field. The resulting many-electron Hamilton operator is forced to be hermitian, but hermiticity is not preserved, in general, for the subsequently derived single-particle operators that determine the electronic orbitals. However, we demonstrate that when focusing on the canonical solutions to the single-particle equations, hermiticity is preserved. The issue of gauge-origin dependence of approximate solutions is addressed. Our approach is compared with several previously proposed treatments, whereby limitations in some of the latter are identified.
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23
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Retracted Article: A highest stable cluster Au 58 ( C 1) re-optimized via a density-functional tight-binding (DFTB) approach. RSC Adv 2018; 8:11357-11366. [PMID: 35542769 PMCID: PMC9079119 DOI: 10.1039/c7ra13171b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/26/2018] [Indexed: 11/21/2022] Open
Abstract
The vibrational spectrum ω i of a re-optimized neutral gold cluster Au58 has been calculated using a numerical finite-difference approach and the density-functional tight-binding (DFTB) method. We have exactly predicted the vibrational frequency ranging from 3.88 through to 304.49 cm-1 which depends on the size and the arrangement of the atoms in the nanoparticle morphology of the cluster at ΔE = 0. Our investigation has revealed that the vibrational spectrum is strongly influenced by size and structure. It is well known that gold atomic clusters can have planar or hollow cage-like structures due to their relativistic effect. However, in our study, by first principles calculations on a Au58 cluster we have proposed that gold clusters of medium size can form a shell-like structure (skeleton/helmet), this is demonstrated by the remarkable robustness of a double shell structure with a hollow inner shell of about ten atoms. Finally, the structure symmetry (C 1) is confirmed through the cluster size, vibrational spectroscopy, and by studying the effect of temperature on a neutral gold cluster for the first time.
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24
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Theoretical study on functionalized anthracene and tetraceneas starting species to produce promising semiconductor materials. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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DFT and MP2 conformational study of 3,6-anhydro-α-d-galactose in gas phase and in aqueous solvent. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Growth patterns, shapes, and electronic properties of mixed Si m Ge n clusters with n+m⩽30. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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30
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Abstract
The contribution of surface units to bulk properties are often neglected in theoretical and computational studies of crystalline systems. We demonstrate that this assumption has to be made with caution in the case of (electric field) polarization.
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31
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Study of the influence of functionalization on the reorganization energy of naphthalene using DFT. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Performance of Hybrid DFT Compared to MP2 Methods in Calculating Nonlinear Optical Properties of Divinylpyrene Derivative Molecules. J Phys Chem A 2016; 120:8843-8852. [PMID: 27749050 DOI: 10.1021/acs.jpca.6b08040] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of divinyl-pyrene derivatives of the form D-vinyl-pyrene-vinyl-A, in which D corresponds to an electron donor group and A to an electron acceptor group, were studied in this work. The first purpose was to determine the optimal HF % exchange as incorporated in a range of hybrid functionals (M06HF, M062X, M06L, CAM-B3LYP, PBE0, BMK, and B3LYP) capable to produce, reliably and as close as possible to those obtained from MP2 calculations, NLO parameters and, in particular, first-order static hyperpolarizabilities. The CAM-B3LYP functional was revealed to be the most suitable one. The pair N(CH3)2/NO2 was then determined as the most efficient pair of groups in producing appreciable NLO responses. The effect of the substitution position on the pyrene moiety was also investigated, whereby aligning the two substituents involving the D and A groups in the direction of the dipole moment as in the (1,6 DVP) derivatives was shown to be most favorable for increasing the NLO parameters.
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Energetic, Structural, and Vibrational Properties of 4,4'-Methylenediphenyl Diisocyanate with Relevance for Adhesion. J Phys Chem A 2016; 120:4256-66. [PMID: 27232061 DOI: 10.1021/acs.jpca.6b04431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Through a polymerization process, the monomer 4,4'-methylenediphenyl diisocyanate can participate in glueing, whereby strong covalent bonds between the monomer and the substrates that will be glued have to be formed. In the present work, we use density functional theory (DFT) calculations to study a group of properties that are important for the initial steps of this process and for its experimental characterization. We focus on energetic and structural properties of a single monomer of 4,4'-methylenediphenyl diisocyanate as obtained using different theoretical approaches. We demonstrate that the molecule is chiral and that for each chirality, three different structures, differing in the orientations of the isocyanate groups, can be identified. The molecule is soft against certain geometry transformations and can, accordingly, easily take a structure that is optimal for the formation of covalent bonds with a substrate. Infrared spectroscopy may be used in identifying these covalent bonds, and therefore, these spectra were calculated, and we identify the most relevant vibrations in this context. Finally, changes in the properties when the monomer was modified or when it was allowed to interact with other molecules were studied, too.
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Magnetostructural phase transition assisted by temperature in Ag-αMnO2: a density functional theory study. Phys Chem Chem Phys 2016; 18:7442-8. [PMID: 26898117 DOI: 10.1039/c5cp08053c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A crystalline material formed by parallel chains of silver atoms inside one-dimensional tunnels of hollandite manganese dioxide, Ag-αMnO2, is investigated through first-principles total energy calculations. Two different magnetic phases have been identified; one structure containing linear Ag chains with an antiferromagnetic ordering in the direction perpendicular to the MnO2 tunnels for T = 0 K (I4/m) and another configuration with zigzag Ag chains in a non-magnetic regime for higher temperatures (P21/c). According to phonon dispersions, both structures are stable. On the other hand, the structure with linear Ag chains in the non-magnetic state is unstable. A critical temperature of Tc≃ 125 K for the magnetostructural phase transition between the two stable structures I4/m and P21/c is predicted.
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Abstract
Abstract
Previously we have determined the lowest-energy structures and full vibrational spectra of
Cu
N
with N up to 150 atoms by means of an unbiased-structure-optimization
approach combined with the analytical formulas of the embedded-atom total-energy method and
the harmonic superposition approximation. Here, we extend the earlier T = 0 studies to T ≠ 0 and present the equilibrium thermodynamic properties of copper clusters with N from 2
to 150. Thereby, we calculate the Helmholtz free energy quantum mechanically and examine
it as a function of temperature and cluster size. It is shown, that the impact of entropic
effects on the stability of the copper clusters is rather small for temperatures less than
300 K, which is about the bulk Debye temperature. For larger temperatures, the
influence of the vibrational entropy on the cluster stability becomes stronger so that with
increasing temperature the stability of some clusters (most often low-symmetrical) is
increased and that of others (most often high-symmetrical) is reduced. For the first time,
we demonstrate the existence of new magic copper clusters at elevated temperatures. These
have the sizes 80, 88, 104, and 125 and will be called the
temperature-dependent magic clusters.
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Growth patterns and structural motifs of cadmium clusters with up to 60 atoms: disordered or not? Phys Chem Chem Phys 2016; 18:28524-28537. [DOI: 10.1039/c6cp04948f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A new growth pattern in small to medium-sized cadmium clusters based on the Leary tetrahedron is predicted.
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Study of structure, energy, and electronic properties of small-sized Si Ge (x+y= 2–8) alloy clusters based on density functional tight binding calculations. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.10.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Site-specific conjugation of 8-ethynyl-BODIPY to a protein by [2 + 3] cycloaddition. Org Biomol Chem 2015; 13:6728-36. [DOI: 10.1039/c5ob00505a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report a straightforward synthesis of 8-ethynyl-BODIPY derivatives and their potential as fluorescent labeling compounds using an alkyne–azide click chemistry approach.
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Theoretical study of the NLO responses of some natural and unnatural amino acids used as probe molecules. J Mol Model 2014; 20:2388. [DOI: 10.1007/s00894-014-2388-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/21/2014] [Indexed: 11/29/2022]
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Electronic responses of long chains to electrostatic fields: Hartree-Fock vs. density-functional theory: a model study. J Chem Phys 2014; 140:054117. [PMID: 24511932 DOI: 10.1063/1.4864038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The response to an electrostatic field is determined through simple model calculations, within both the restricted Hartree-Fock and density functional theory methods, for long, finite as well as infinite, periodic chains. The permanent dipole moment, μ0, the polarizability, α, and the hyperpolarizabilities β and γ, calculated using a finite-field approach, are extensively analyzed. Our simple model allows for treatment of large systems and for separation of the properties into atomic and unit-cell contributions. That part of the response properties attributable to the terminations of the finite system change into delocalized current contributions in the corresponding infinite periodic system. Special emphasis is placed on analyzing the reasons behind the dramatic overestimation of the response properties found with density functional theory methods presently in common use.
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Abstract
Chemical bonding in and electronic structure of lithium and magnesium rhodium hydrides are studied theoretically using DFT methods. For Li3RhH4 with planar complex RhH4 structural units, Crystal Orbital Hamilton Populations reveal significant Rh−Rh interactions within infinite one-dimensional ∞ 1 [RhH4] stacks in addition to strong rhodium−hydrogen bonding. These metal−metal interactions are considerably weaker in the hypothetical, heavier homologue Na3RhH4. Both compounds are small-band gap semiconductors. The electronic structures of Li3RhH6 and Na3RhH6 with rhodium surrounded octahedrally by hydrogen, on the other hand, are compatible with a classical complex hydride model according to the limiting ionic formula (M+)3[RhH6]3− without any metal−metal interaction between the 18-electron hydridorhodate complexes. In MgRhH, building blocks of the composition (RhH2)4 are formed with strong rhodium−hydrogen and significant rhodium−rhodium bonding (bond lengths of 298 pm within Rh4 squares). These units are linked together to infinite two-dimensional layers ∞ 2 [(RhH2/2)4] via common hydrogen atoms. Li3RhH4 and MgRhH are accordingly examples for border cases of chemical bonding where the classical picture of hydridometalate complexes in complex hydrides is not sufficient to properly describe the chemical bonding situation.
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On Aliovalent Substitution on the Li Site in LiMPO4: an X-ray Diffraction Study of the Systems LiMPO4-M1.5PO4(= LixM1.5-x/2PO4; M = Ni, Co, Fe, Mn). Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Clusters: From dimers to nanoparticles. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Building band structures for long finite chains in presence of an electric field. J Chem Phys 2013; 137:144108. [PMID: 23061840 DOI: 10.1063/1.4757118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
At first, three different methods devoted to extracting the periodic-system band structures from the results of finite-system calculations are being discussed. Special emphasis is put on the performance of these methods for a system that is exposed to an external electrostatic field. Using model calculations we found that the three methods converge to the same results in the absence of the electrostatic field, but they lead to small differences when the field is included, which can be ascribed to distortions of the spatial extensions of the orbitals generated by the field. These small differences become important when addressing the issue whether it is possible to identify uniquely a set of band structures for the infinite, periodic system exposed to an electrostatic field. This question, related to the question whether the phases of the periodic-system orbitals are of physical importance, has so far not been answered. Applying the results of the first part we ultimately suggest that it is not possible to identify a unique set of band structures when the periodic system is exposed to an electrostatic field.
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Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water. J Mol Model 2012; 19:893-904. [PMID: 23086461 DOI: 10.1007/s00894-012-1621-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.
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Neutron and X-ray diffraction studies on the high temperature phase of Mn3(VO4)2, the new isostructural compound NaMn4(VO4)3 and their mixed crystals Na Mn4.5−/2(VO4)3 (0≤x≤1). J SOLID STATE CHEM 2012. [DOI: 10.1016/j.jssc.2012.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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TiO2 cellular-protected nanowire array fabricated super-rapidly by the precipitation of colloids in the nanopores. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31255g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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A DFT study of the properties of substituted pyrrolidines and phospholanes in gas and in aqueous phase. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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