18 results on '"Schaefer HF 3rd"'
Search Results
2. Conformers, properties, and docking mechanism of the anticancer drug docetaxel: DFT and molecular dynamics studies.
- Author
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Sun C, Zhu L, Zhang C, Song C, Wang C, Zhang M, Xie Y, and Schaefer HF 3rd
- Subjects
- Molecular Conformation, Antineoplastic Agents chemistry, Density Functional Theory, Docetaxel chemistry, Molecular Docking Simulation, Molecular Dynamics Simulation
- Abstract
The conformational structures and properties of the anticancer drug docetaxel (DTX) are studied theoretically. A total of 3888 trial structures were initially generated by all combinations of internal single-bond rotamers and screened with the B3LYP/3-21G* method. A total of 31 unique conformers were further optimized at the B3LYP/6-311G* method. Their relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies were predicted. Single-point relative energies were then determined at the M06-L/6-311G(2df,p) level. The UV spectrum of the lowest-lying DTX conformer in methanol was investigated with the TD-CAM-B3LYP/6-311 + G(2df,p) method. The 31 unique DTX structures are mainly docked at three different sites within β-tubulin. Based on the results of molecular docking and double-float MD simulations, the lowest-lying DTX conformer consistently exhibits good docking performance with β-tubulin. We identified the residues LYS299, ARG215, GLN294, LEU275, THR216, GLU290, PRO274, and THR276 on β-tubulin as active sites forming a binding pocket responsible for locking DTX within β-tubulin to make the combination more stable. The RMSD values show that the predicted complexes are favorable, and the SASA analysis shows that the hydrophilic properties of DTX are better than paclitaxel. © 2018 Wiley Periodicals, Inc., (© 2018 Wiley Periodicals, Inc.)
- Published
- 2018
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3. Hyperconjugative effects in π-hydrogen bonding: Theory and experiment.
- Author
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Galabov B, Nikolova V, Cheshmedzhieva D, Hadjieva B, and Schaefer HF 3rd
- Abstract
Density functional theory computations with the B3LYP/6-311++G(2df,2p) method and IR spectroscopy are employed in investigating the properties of twenty π-hydrogen bonded complexes between substituted phenols and hexamethylbenzene. All complexes possess T-shaped structures. The methyl hyperconjugative effects on interactions energies and OH stretching frequencies are estimated via comparisons with previously reported theoretical and experimental results for analogous phenol complexes with benzene. The theoretical computations provide excellent quantitative predictions of the OH stretching frequency shifts (Δν
OH ) resulting from the hydrogen bonding. The ΔνOH shifts in the hexamethylbenzene complexes are approximately twice as large as the corresponding shifts for the benzene complexes. Hirshfeld charges, electrostatic potential at nuclei values, and molecular electrostatic potential maps are employed in gaining insights into the mechanisms of methyl hyperconjugative effects on complex formation. © 2017 Wiley Periodicals, Inc., (© 2017 Wiley Periodicals, Inc.)- Published
- 2018
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4. Bis(azulene) "submarine" metal dimer sandwich compounds (C10H8)2M2(M = Ti, V, Cr, Mn, Fe, Co, Ni): Parallel and opposed orientations.
- Author
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Wang H, Wang H, King RB, and Schaefer HF 3rd
- Abstract
The opposed and parallel structures for the binuclear bis(azulene) "submarine" sandwiches (C10H8)2M2 (M = Ti, V, Cr, Mn, Fe, Co, Ni) have been optimized using density functional theory. The lowest energy (C10H8)2 M2 structures of the early transition metals Ti, V, Cr, and Mn have the azulene units functioning as bis(pentahapto) ligands to each metal atom similar to the azulene ligand in the long-known molybdenum carbonyl complex (η(5),η(5)-C10H8 )Mo2 (CO)6 . The metal-metal bonds in these early transition metal structures have distances and Wiberg bond indices consistent with the formal bond orders required to give each metal atom an 18-electron configuration for the singlet structures and a 17-electron configuration for the triplet structures. For the later transition metals Fe, Co, and Ni, the lowest energy (C10H8)2 M2 structures contain pentahapto-trihapto azulene ligands with an uncomplexed C=C double bond, similar to that in the long-known iron carbonyl complex (η(5),η(3)-C10H8)Fe2 (CO)5 . The parallel (η(5),η(3)-C10H8 )2M2 (M = Fe, Co, Ni) structures contain metallocene subunits with their metal atoms at long nonbonding distances of 3.5-3.9 Å from the other metal atom, which is located between the azulene C7 rings. Higher energy opposed (C10H8)2 Fe2 structures contain an unprecedented distorted η(6) ,η(4) -azulene ligand using six carbon atoms for bonding to one iron atom as a hexahapto fulvene ligand and the remaining four carbon atoms for bonding to the other iron atom as a tetrahapto diene ligand., (© 2015 Wiley Periodicals, Inc.)
- Published
- 2016
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5. The Reaction between Bromine and the Water Dimer and the Highly Exothermic Reverse Reaction.
- Author
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Li G, Wang H, Li QS, Xie Y, and Schaefer HF 3rd
- Abstract
The entrance complex, transition state, and exit complex for the bromine atom plus water dimer reaction Br + (H2O)2 → HBr + (H2O)OH and its reverse reaction have been investigated using the CCSD(T) method with correlation consistent basis sets up to cc-pVQZ-PP. Based on the CCSD(T)/cc-pVQZ-PP results, the reaction is endothermic by 31.7 kcal/mol. The entrance complex Br⋯(H2O)2 is found to lie 6.5 kcal/mol below the separated reactants. The classical barrier lies 28.3 kcal/mol above the reactants. The exit complex HBr⋯(H2O)OH is bound by 6.0 kcal/mol relative to the separated products. Compared with the corresponding water monomer reaction Br + H2 O → HBr + OH, the second water molecule lowers the relative energies of the entrance complex, transition state, and exit complex by 3.0, 3.8, and 3.7 kcal/mol, respectively. Both zero-point vibrational energies and spin-orbit coupling effects make significant changes to the above classical energetics. Including both effects, the predicted energies relation to separated Br + (H2O)2 are -3.0 kcal/mol [Br···(H2O)2 ], 28.2 kcal/mol [transition state], 26.4 kcal/mol [HBr···(H2O)OH], and 30.5 kcal/mol [separated HBr + (H2O)OH]. The potential energy surface for the Br + (H2O)2 reaction is related to that for the valence isoelectronic Cl + (H2O)2 system but radically different from the F + (H2O)2 system., (© 2015 Wiley Periodicals, Inc.)
- Published
- 2016
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6. Hydrogen bond-aromaticity cooperativity in self-assembling 4-pyridone chains.
- Author
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Anand M, Fernández I, Schaefer HF 3rd, and Wu JI
- Abstract
Self-assembling building blocks like the 4-pyridone can exhibit extraordinary H-bond-aromaticity coupling effects. Computed dissected nucleus independent chemical shifts (NICS(1)zz), natural bond orbital (NBO) charges, and energy decomposition analyses (EDA) for a series of hydrogen (H-) bonded 4-pyridone chains (4-py)n (n = 2 to 8) reveal that H-bonding interactions can polarize the 4-pyridone exocyclic C=O bonds and increase 4n+2 π-electron delocalization in the six-membered ring. The resulting H-bonded 4-pyridone units display enhanced π-aromatic character (both magnetically and energetically) and their corresponding N-H···O=C interactions are strengthened. These π-electron polarization effects do not depend on the relative orientations (co-planar or perpendicular) of the neighboring 4-pyridone units, but increase with the number of H-bonded units., (© 2015 Wiley Periodicals, Inc.)
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- 2016
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7. Catenanes: A molecular mechanics analysis of the (C13H26)2 Structure 13-13 D2.
- Author
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Lii JH, Allinger NL, Hu CH, and Schaefer HF 3rd
- Abstract
Molecular mechanics (MM4) studies have been carried out on the catenane (C13H26)2, specifically 13-13D2. The structure obtained is in general agreement with second-order perturbation theory. More importantly, the MM4 structure allows a breakdown of the energy of the molecule into its component classical parts. This allows an understanding of why the structure is so distorted, in terms of C-C bonding and nonbonding interactions, van der Waals repulsion, C-C-C and C-C-H angle bending, torsional energies, stretch-bend, torsion-stretch, and bend-torsion-bend interactions. Clearly, the hole in 113-membered ring is too small for the other ring to fit through comfortably. There are too many atoms trying to fit into the limited space at the same time, leading to large van der Waals repulsions. The rings distort in such a way as to enlarge this available space, and lower the total energy of the molecule. While the distortions are spread around the rings, one of the nominally tetrahedral C-C-C bond angles in each ring is opened to 147.9° by MM4 (146.8° by MP2). The stability of the compound is discussed in terms of the strain energy., (© 2015 Wiley Periodicals, Inc.)
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- 2016
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8. The reactions of Cr(CO)6, Fe(CO)5, and Ni(CO)4 with O2 yield viable oxo-metal carbonyls.
- Author
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Sun Z, Schaefer HF 3rd, Xie Y, Liu Y, and Zhong R
- Subjects
- Quantum Theory, Carbon Monoxide chemistry, Chromium chemistry, Iron chemistry, Nickel chemistry, Oxygen chemistry
- Abstract
Transition metal complexes with terminal oxo and dioxygen ligands exist in metal oxidation reactions, and many are key intermediates in various catalytic and biological processes. The prototypical oxo-metal [(OC)5Cr-O, (OC)4Fe-O, and (OC)3 Ni-O] and dioxygen-metal carbonyls [(OC)5Cr-OO, (OC)4Fe-OO, and (OC)3Ni-OO] are studied theoretically. All three oxo-metal carbonyls were found to have triplet ground states, with metal-oxo bond dissociation energies of 77 (Cr-O), 74 (Fe-O), and 51 (Ni-O) kcal/mol. Natural bond orbital and quantum theory of atoms in molecules analyses predict metal-oxo bond orders around 1.3. Their featured ν(MO, M = metal) vibrational frequencies all reflect very low IR intensities, suggesting Raman spectroscopy for experimental identification. The metal interactions with O2 are much weaker [dissociation energies 13 (Cr-OO), 21 (Fe-OO), and 4 (Ni-OO) kcal/mol] for the dioxygen-metal carbonyls. The classic parent compounds Cr(CO)6, Fe(CO)5, and Ni(CO)4 all exhibit thermodynamic instability in the presence of O2 , driven to displacement of CO to form CO2. The latter reactions are exothermic by 47 [Cr(CO)6], 46 [Fe(CO)5], and 35 [Ni(CO)4] kcal/mol. However, the barrier heights for the three reactions are very large, 51 (Cr), 39 (Fe), and 40 (Ni) kcal/mol. Thus, the parent metal carbonyls should be kinetically stable in the presence of oxygen., (Copyright © 2014 Wiley Periodicals, Inc.)
- Published
- 2014
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9. Structural and electronic property responses to the arsenic/phosphorus exchange in GC-related DNA of the B-form.
- Author
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Gu J, Wang J, Xie Y, Leszczynski J, and Schaefer HF 3rd
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- Base Pairing, Cytosine chemistry, Deoxycytosine Nucleotides chemistry, Deoxyguanosine analogs & derivatives, Deoxyguanosine chemistry, Electrons, Guanine chemistry, Hydrogen Bonding, Models, Molecular, Nucleic Acid Conformation, Arsenic chemistry, DNA chemistry, GC Rich Sequence, Phosphorus chemistry
- Abstract
The suggestion that phosphorus/arsenic replacement in DNA can play a role in living things has generated great controversy (Wolfe-Simon et al., Science 2011, 332, 1163). Examined here theoretically are substitution effects on Watson-Crick base pairing and base stacking patterns in realistic DNA subunits. Using duplex DNA models deoxyguanylyl-3',5'-deoxycytidine ([dGpdC](2) ) and deoxycytidyly-3',5'-deoxyguanosine ([dCpdG)](2) ), this research reveals that the geometric variations caused by the As/P exchange are small and are limited to the phosphate/arsenate groups. As/P replacement leads to alterations of ∼0.15 Å in P/AsO bond lengths and less than 1.5° variations in OP/AsO angles. The Watson-Crick base pairing and base stacking patterns are independent of the As/P replacement. The vertical electron detachment energies are also largely unaffected. However, the electron capture ability of the DNA units is improved by the As substitution. The arsenate is found to be the main electron acceptor in As-DNA. The results are relevant to the possible existence of viable As-DNAs, at least in the guanine and cytosine (GC)-related B-form DNA., (Copyright © 2012 Wiley Periodicals, Inc.)
- Published
- 2012
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10. From acetylene complexes to vinylidene structures: The GeC(2) H(2) system.
- Author
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Hao Q, Simmonett AC, Yamaguchi Y, Fang DC, and Schaefer HF 3rd
- Abstract
The expansion of germanium chemistry in recent years has been rapid. In anticipation of new experiments, a systematic theoretical investigation of the eight low lying electronic singlet GeC(2) H(2) stationary points is carried out. This research used ab initio self-consistent-field (SCF), coupled cluster (CC) with single and double excitations (CCSD), and CCSD with perturbative triple excitations [CCSD(T)] levels of theory and a variety of correlation-consistent polarized valence cc-pVXZ and cc-pVXZ-DK (Douglas-Kroll) (where X = D, T, and Q) basis sets. At all levels of theory used in this study, the global minimum of the GeC(2) H(2) potential energy surface (PES) is confirmed to be 1-germacyclopropenylidene (Ge-1S). Among the eight singlet stationary points, seven structures are found to be local minima and one structure (Ge-6S) to be a second-order saddle point. For the seven singlet minima, the energy ordering and energy differences (in kcal mol(-1) , with the zero-point vibrational energy corrected values in parentheses) at the cc-pVQZ-DK (Douglas-Kroll) CCSD(T) level of theory are predicted to be 1-germacyclopropenylidene (Ge-1S) [0.0 (0.0)] < vinylidenegermylene (Ge-3S) [13.9 (13.5)] < ethynylgermylene (Ge-2S) [17.9 (14.8)] < Ge-7S [37.4 (33.9)] < syn-3-germapropenediylidene (Ge-8S) [41.2 (37.9)] < germavinylidenecarbene (Ge-5S) [66.6 (61.6)] < nonplanar germacyclopropyne (Ge-4S) [67.8 (63.3)]. These seven isomers are all well below the dissociation limit to Ge ((3) P) + C(2) H(2) (X (1) Σ g+). This system seems particularly well poised for matrix isolation infrared (IR) experiments., (Copyright © 2010 Wiley Periodicals, Inc.)
- Published
- 2011
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11. Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations.
- Author
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Woodcock HL 3rd, Hodošček M, Gilbert ATB, Gill PMW, Schaefer HF 3rd, and Brooks BR
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- Anions chemistry, Catalysis, Chorismate Mutase metabolism, Computer Simulation, Dimerization, Models, Molecular, Protein Structure, Tertiary, Quantum Theory, Sodium chemistry, Water chemistry, Models, Chemical, Software
- Abstract
A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory., (Copyright (c) 2007 Wiley Periodicals, Inc.)
- Published
- 2007
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12. Molecular structures of the two most stable conformers of free glycine.
- Author
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Kasalová V, Allen WD, Schaefer HF 3rd, Czinki E, and Császár AG
- Subjects
- Computer Simulation, Electrons, Models, Molecular, Molecular Structure, Vibration, Glycine chemistry
- Abstract
The equilibrium molecular structures of the two lowest-energy conformers of glycine, Gly-Ip and Gly-IIn, have been characterized by high-level ab initio electronic structure computations, including all-electron cc-pVTZ CCSD(T) geometry optimizations and 6-31G* MP2 quartic force fields, the latter to account for anharmonic zero-point vibrational effects to isotopologic rotational constants. Based on experimentally measured vibrationally averaged effective rotational constant sets of several isotopologues and our ab initio data for structural constraints and zero-point vibrational shifts, least-squares structural refinements were performed to determine improved Born-Oppenheimer equilibrium (r(e)) structures of Gly-Ip and Gly-IIn. Without the ab initio constraints even the extensive set of empirical rotational constants available for 5 and 10 isotopologues of Gly-Ip and Gly-IIn, respectively, cannot satisfactorily fix their molecular structure. Excellent agreement between theory and experiment is found for the rotational constants of both conformers, the rms residual of the final fits being 7.8 and 51.6 kHz for Gly-Ip and Gly-IIn, respectively. High-level ab initio computations with focal point extrapolations determine the barrier to planarity separating Gly-IIp and Gly-IIn to be 20.5 +/- 5.0 cm(-1). The equilibrium torsion angle tau(NCCO) of Gly-IIn, characterizing the deviation of its heavy-atom framework from planarity, is (11 +/- 2) degrees. Nevertheless, in the ground vibrational state the effective structure of Gly-IIn has a plane of symmetry.
- Published
- 2007
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13. The existence of secondary orbital interactions.
- Author
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Wannere CS, Paul A, Herges R, Houk KN, Schaefer HF 3rd, and von Ragué Schleyer P
- Abstract
B3LYP/6-311+G** (and MP2/6-311+G**) computations, performed for a series of Diels-Alder (DA) reactions, confirm that the endo transition states (TS) and the related Cope-TSs are favored energetically over the respective exo-TSs. Likewise, the computed magnetic properties (nucleus-independent chemical shifts and magnetic susceptibililties) of the endo- (as well as the Cope) TS's reveal their greater electron delocalization and greater aromaticity than the exo-TS's. However, Woodward and Hoffmann's original example is an exception: their endo-TS model, involving the DA reaction of a syn- with an anti-butadiene (BD), actually is disfavored energetically over the corresponding exo-TS; magnetic criteria also do not indicate the existence of SOI delocalization in either case. Instead, a strong energetic preference for endo-TSs due to SOI is found when both BDs are in the syn conformations. This is in accord with Alder and Stein's rule of "maximum accumulation of double bonds:" both the dienophile and the diene should have syn conformations. Plots along the IRC's show that the magnetic properties typically are most strongly exalted close to the energetic TS. Because of SOI, all the points along the endo reaction coordinates are more diatropic than along the corresponding exo pathways. We find weak SOI effects to be operative in the endo-TSs involved in the cycloadditions of cyclic alkenes, cyclopropene, aziridine, cyclobutene, and cyclopentene, with cyclopentadiene. While the endo-TSs are only slightly lower in energy than the respective exo-TSs, the magnetic properties of the endo-TS's are significantly exalted over those for the exo-TS's and the Natural Bond Orbitals indicate small stabilizing interactions between the methylene cycloalkene hydrogen orbitals (and lone pairs in case of aziridine) with pi-character and the diene pi MOs., (Copyright (c) 2006 Wiley Periodicals, Inc.)
- Published
- 2007
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14. The ab initio limit quartic force field of BH3.
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Schuurman MS, Allen WD, and Schaefer HF 3rd
- Abstract
The complete quartic force field of BH(3) has been converged to the ab initio limit by extrapolation of core-valence correlation-consistent basis set series (cc-pCVXZ, X = T, Q, 5) of all-electron CCSD(T) (coupled-cluster singles and doubles with perturbative triples) energy points. Additional computations including full coupled-cluster treatments through quadruple excitations (CCSDTQ), scalar relativistic effects, and diagonal Born-Oppenheimer corrections (DBOC) were concurrently executed. Within second-order vibrational perturbation theory (VPT2) our quartic force field yields the fundamental frequencies nu(1) = 2502.3 cm(-1), nu(2) = 1147.2 cm(-1), nu(3) = 2602.1 cm(-1), and nu(4) = 1196.5 cm(-1), in excellent agreement with observed gas-phase fundamentals, displaying a mean absolute error of only 0.3 cm(-1). Our converged prediction for the equilibrium bond length of BH(3) is r(e) = 1.1867 A., ((c) 2005 Wiley Periodicals, Inc.)
- Published
- 2005
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15. Structures and electron affinities of the di-arsenic fluorides As2Fn/As2Fn- (n=1-8).
- Author
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Kasalová V and Schaefer HF 3rd
- Abstract
Developments in the preparation of new materials for microelectronics are focusing new attention on molecular systems incorporating several arsenic atoms. A systematic investigation of the As2Fn/As2Fn- systems was carried out using Density Functional Theory methods and a DZP++ quality basis set. Global and low-lying local geometric minima and relative energies are discussed and compared. The three types of neutral-anion separations reported in this work are: the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). Harmonic vibrational frequencies pertaining to the global minimum for each compound are reported. From the first four studied species (As2Fn, n=1-4), all neutral molecules and their anions are shown to be stable with respect to As-As bond breaking. The neutral As2F molecule and its anion are predicted to have Cs symmetry. We find the trans F-As-As-F isomer of C2h symmetry and a pyramidalized vinylidene-like As-As-F2- isomer of Cs symmetry to be the global minima for the As2F2 and As2F2- species, respectively. The lowest lying minima of As2F3 and As2F3- are vinyl radical-like structures F-As-As-F2 of Cs symmetry. The neutral As2F4 global minimum is a trans-bent (like Si2H4) F2-As-As-F2 isomer of C2 symmetry, while its anion is predicted to have an unusual fluorine-bridged (C(1)) structure. The global minima of the neutral As2Fn species, n=5-8, are weakly bound complexes, held together by dipole-dipole interactions. All such structures have the AsFm-AsFn form, where (m,n) is (2,3) for As2F5, (3,3) for As2F6, (4,3) for As2F7), and (5,3) for As2F8. For As2F8 the beautiful pentavalent F4As-AsF4 structure (analogous to the stable AsF5 molecule) lies about 30 kcal/mol above the AsF3 . . . AsF5 complex. The stability of AsF(5) depends crucially on the strong As-F bonds, and replacing one of these with an As-As bond (in F4As-AsF4) has a very negative impact on the molecule's stability. The anions As2Fn-, n=5-8, are shown to be stable with respect to the As-As bond breaking, and we predict that all of them have fluorine-bridged or fluorine-linked structures. The zero-point vibrational energy corrected adiabatic electron affinities are predicted to be 2.28 eV (As2F), 1.95 eV (As2F2), 2.39 eV (As2F3), 1.71 eV (As2F4), 2.72 eV (As2F5), 1.79 eV (As2F6), 5.26 eV (As2F7), and 3.40 eV (As2F8) from the BHLYP method. Vertical detachment energies are rather large, especially for species with fluorine-bridged global minima, having values up to 6.45 eV (As2F7, BHLYP).
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- 2005
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16. The arsenic clusters Asn (n = 1-5) and their anions: structures, thermochemistry, and electron affinities.
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Zhao Y, Xu W, Li Q, Xie Y, and Schaefer HF 3rd
- Abstract
The molecular structures, electron affinities, and dissociation energies of the As(n)/As(-) (n) (n = 1-5) species have been examined using six density functional theory (DFT) methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. These methods have been carefully calibrated (Chem Rev 2002, 102, 231) for the prediction of electron affinities. The geometries are fully optimized with each DFT method independently. Three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). The first dissociation energies D(e)(As(n-1)-As) for the neutral As(n) species, as well as those D(e)(As(-) (n-1)-As) and D(e) (As(n-1)-As(-)) for the anionic As(-) (n) species, have also been reported. The most reliable adiabatic electron affinities, obtained at the DZP++ BLYP level of theory, are 0.90 (As), 0.74 (As(2)), 1.30 (As(3)), 0.49 (As(4)), and 3.03 eV (As(5)), respectively. These EA(ad) values for As, As(2), and As(4) are in good agreement with experiment (average absolute error 0.09 eV), but that for As(3) is a bit smaller than the experimental value (1.45 +/- 0.03 eV). The first dissociation energies for the neutral arsenic clusters predicted by the B3LYP method are 3.93 eV (As(2)), 2.04 eV (As(3)), 3.88 eV (As(4)), and 1.49 eV (As(5)). Compared with the available experimental dissociation energies for the neutral clusters, the theoretical predictions are excellent. Two dissociation limits are possible for the arsenic cluster anions. The atomic arsenic results are 3.91 eV (As(-) (2) --> As(-) + As), 2.46 eV (As(-) (3) --> As(-) (2) + As), 3.14 eV (As(-) (4) --> As(-) (3) + As), and 4.01 eV (As(-) (5) --> As(-) (4) + As). For dissociation to neutral arsenic clusters, the predicted dissociation energies are 2.43 eV (As(-) (3) --> As(2) + As(-)), 3.53 eV (As(-) (4) --> As(3) + As(-)), and 3.67 eV (As(-) (5) --> As(4) + As(-)). For the vibrational frequencies of the As(n) series, the BP86 and B3LYP methods produce good results compared with the limited experiments, so the other predictions with these methods should be reliable., (Copyright 2004 Wiley Periodicals, Inc.)
- Published
- 2004
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17. Molecules for materials: germanium hydride neutrals and anions. Molecular structures, electron affinities, and thermochemistry of GeHn/GeHn- (n = 0-4) and Ge2Hn/Ge2Hn(-) (n = 0-6).
- Author
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Li QS, Lü RH, Xie Y, and Schaefer HF 3rd
- Abstract
The GeH(n) (n = 0-4) and Ge(2)H(n) (n = 0-6) systems have been studied systematically by five different density functional methods. The basis sets employed are of double-zeta plus polarization quality with additional s- and p-type diffuse functions, labeled DZP++. For each compound plausible energetically low-lying structures were optimized. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews 102, 231, 2002). The geometries predicted in this work include yet unknown anionic species, such as Ge(2)H(-), Ge(2)H(2)(-), Ge(2)H(3)(-), Ge(2)H(4)(-), and Ge(2)H(5)(-). In general, the BHLYP method predicts the geometries closest to the few available experimental structures. A number of structures rather different from the analogous well-characterized hydrocarbon radicals and anions are predicted. For example, a vinylidene-like GeGeH(2) (-) structure is the global minimum of Ge(2)H(2) (-). For neutral Ge(2)H(4), a methylcarbene-like HGë-GeH(3) is neally degenerate with the trans-bent H(2)Ge=GeH(2) structure. For the Ge(2)H(4) (-) anion, the methylcarbene-like system is the global minimum. The three different neutral-anion energy differences reported in this research are: the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). For this family of molecules the B3LYP method appears to predict the most reliable electron affinities. The adiabatic electron affinities after the ZPVE correction are predicted to be 2.02 (Ge(2)), 2.05 (Ge(2)H), 1.25 (Ge(2)H(2)), 2.09 (Ge(2)H(3)), 1.71 (Ge(2)H(4)), 2.17 (Ge(2)H(5)), and -0.02 (Ge(2)H(6)) eV. We also reported the dissociation energies for the GeH(n) (n = 1-4) and Ge(2)H(n) (n = 1-6) systems, as well as those for their anionic counterparts. Our theoretical predictions provide strong motivation for the further experimental study of these important germanium hydrides., (Copyright 2002 Wiley Periodicals, Inc.)
- Published
- 2002
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18. From "parasitic" association reactions toward the stoichiometry controlled gas phase synthesis of nanoparticles: a theoretically driven challenge for experimentalists.
- Author
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Timoshkin AY and Schaefer HF 3rd
- Abstract
In the present record a model for the gas-phase reactions during the chemical vapor deposition (CVD) processes of group 13-15 materials is presented, based on the results of extensive quantum-chemical modeling. Thermodynamic criteria have been introduced to evaluate the importance of a range of association reactions. For the organometallic and hydride derivatives, association processes are found to be favorable both thermodynamically and kinetically. Formation of high mass association products takes place under CVD conditions, including laser-assisted CVD. Structural and thermodynamic properties of the most important ring and cluster intermediates have been predicted. The stoichiometry-controlled synthesis of the 13-15 ternary alloys and nanoparticles using cluster compounds as single-source precursors is predicted to be viable. The association pathway described may be generalized to the CVD reactions of many binary materials (12-16, 13-16, 13-15, 14-15, 14-16)., (Copyright 2002 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 2: 319-338, 2002: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.10037)
- Published
- 2002
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