The MM3 force field for 12-vertex boranes and carboranes

Timofeeva, T. V.; Suponitsky, Kyrill Yu.; Yanovsky, A.I.; Allinger, Norman L.

doi:10.1016/s0022-328x(96)06819-2

Cited by 26 publications

(34 citation statements)

References 24 publications

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“…Such pronounced elongation of those bonds can be explained by the transfer of the electron density from the sulfur lone pair to the carborane cage 12 as well as by high lability of the bonds of the carborane cage. 13 The C carb -S bonds in 3 are somewhat longer than the similar bonds in the related closo-carborane 1 (1.7610(13) and 1.7630(14) Å), 14 which can be considered as additional evidence of weaker electron-withdrawing properties of the nidocarborane cage and the stronger donor ability of the ligand.…”

Section: Resultsmentioning

confidence: 99%

“…Recently we demonstrated that the δ SMe signals in the 1 H and 13 C NMR spectra of tungsten carbonyl complexes with nido-carboranyl methylsulfide ligands [(CO) 5 W(MeSCarb)] could serve as an indicator of their donor properties. 6 In this contribution we describe the synthesis of tungsten carbonyl complexes with neutral charge-compensated nido-carboranyl methylsulfide ligands [7-MeS-…”

Section: Introductionmentioning

confidence: 99%

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Tungsten carbonyl σ-complexes with charge-compensated nido-carboranyl thioether ligands

et al. 2015

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Charge-compensated nido-carboranyl thioether ligands [7-MeS-10-Me2S-7,8-C2B9H10] and [7,8-(MeS)2-10-Me2S-7,8-C2B9H9] were prepared and fully characterized. They readily react with labile tungsten carbonyls to give σ-complexes - mono-substituted (CO)5W[7-MeS-10-Me2S-7,8-C2B9H10-κ(1)-S(1)] and (CO)5W[7,8-(MeS)2-10-Me2S-7,8-C2B9H9-κ(1)-S(1)] and chelate (CO)4W[7,8-(MeS)2-10-Me2S-7,8-C2B9H9-κ(2)-S(1),S(2)]. The synthesized metallocomplexes were characterized by multinuclear NMR spectroscopy and single crystal X-ray diffraction. The donor ability of the 7-methylsulfide-nido-carborane ligand is not sensitive to introduction of the charge-compensating dimethylsulfonium group.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Tungsten carbonyl σ-complexes with charge-compensated nido-carboranyl thioether ligands

et al. 2015

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“…Therefore, with the aim of performing conformational analysis of the above-mentioned metallacarboranes, we have developed a model and constructed the parameter set based on the concepts that form the basis of the molecular mechanics description of ~-cyclopentadienyl complexes of transition metals, 6,7 sandwich complexes (R2C2B4H4)2M (M = Si, Ge, or Sn), s and 12-vertex closo-carboranes. 9 The results of calculations demonstrated that the structures of these molecules are adequately described within the framework of the molecular mechanics method and can be adequately explained by steric effects.…”

Section: Description Of the Model And Calculation Proceduresmentioning

confidence: 91%

“…The interactions between the five-membered fragments and the apical B atom in the nS-dicarbollyl ligand are analogous to the corresponding interactions in 12-vertex closo-carboranes, which have been discussed in detail previously. 9 The geometric parameters of complexes 1--4, which have been studied by X-ray diffraction analysis, I-4 were used for describing the bonds in the Rah--nS-dicarbollyl and Rh--n2,3-norbornadienyl ligands. Based on these data, we carried out a statistical analysis of the R.h--Y bond lengths (Y are the C or B atoms of the pentagonal plane of the ~5-dicarbollyl ligand, the C atoms at the double bond, or the C atoms of the allyl fragment of the n2,3-norbomadienyl ligand) as well as of the C--C bond lengths and bond angles in the n2,3-norbomadienyl ligand.…”

Section: Description Of the Model And Calculation Proceduresmentioning

confidence: 99%

Conformational analysis of mono- and di-C-substituted derivatives ofcloso-3,3-[η2,3-(2-methylenebicyclo[2.2.1]hepta-2,5-dien-2-yl)]-1-R-2-R1-3,1,2-dicarbollylrhodium (R and R1=h, Me, or PhCH2)-(2-methylenebicyclo[2.2.1]hepta-2,5-dien-2-yl)]-1-R-2-R1-3,1,2-dicarbollylrhodium (R and R1=h, Me, or PhCH2)

et al. 1998

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A model has been developed that allows one to carry out molecular mechanics calculations of metallacarborane complexes with various ligands with the use of the MM3 program package. Based on X-ray structural data on a number of rhodium complexes in which the rhodium atom is coordinated by the ~12.3-norbomadienyl and rlS-dicarbollyl ligands, a parameter set was developed for the compounds of the above-mentioned series. The use of this model made it possible to study the effects of various factors on the structures of theKey words: molecular mechanics, closo-rhodacarboranes, stereochernistry.An important characteristic feature of the nS-dicarbollyl ligand is the absence of symmetry, in its monosubstituted derivatives that contain substituents at C atoms and some B atoms. Therefore, the presence of an additional asymmetrical center in mono-C-substi- The single-crystal X-ray diffraction study of two pairs of the diastereomers, (RS/SR)-and (SS/RR)-closo-3,3-(rl2,3-CTHTCH2)-I-R-3,1,2-RhC2BgHt0 (la,b, R = PhCH2; 3 and 2a,b, R = Me),* made it possible to find an interesting dependence of the solid-state conformation of the norbomadienyl ligand on the stereochemical configuration of the diastereomeric complexes. Thus, in isomers la and 2a, which have RS/SR relative configurations, the norbomadienyl ligand is oriented so that its allylic moiety is projected onto the pentagonal C2B 3 plane of the ~15-dicarbollyl ligand and screens the C(2) and B (7) atoms. In the diastereomers with the opposite configuration (lb and 2b), this group is located approximately above the B(8)--B(4) bond (see below). It is interesting that in the solid state the hydrocarbon ligand in the complex, closo-3,3-(r~2'LC7HTCH2)-3,1,2-RhC2BgHII (3) (three independent molecules), 4 and in its 1,2-dimethyl derivative, closo-3,3-(~2.3-C7HTCH2) -1,2-Me2-3 , 1,2-R_hC2BgH 9 (4), t adopts a conformation similar to that observed for isomers la and 2a in spite of the fact that in compound 4 the distance between the exocyclic C atom of the norbornadienyl ligand and the C atom of the nearest methyl substituent in the ~lS-dicarboUyl Iigand is 3.074 A, Le., it is substantially smaller that the sum of the van der Waals radii of the C atoms (3.4 k).

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“…Molecular dynamics simulations were performed with the GROMACS molecular dynamics simulation package [12] using the AMBER force field parm94 [13] and the TIP3P water model. The force field parameters for ortho -carborane appropriate for use with Amber 99 were obtained from Sarosi et al [14] which were adapted from the bond stretching and torsion parameters developed from HF/6–31 + G* optimization and GAFF values by Timofeeva et al [15] and from the bonded terms developed by Gamba et al [16] . The partial charges on boron, carbon, and hydrogen were obtained from closo -carboranyl antifolate models [17] generated using electrostatic potential fitting in Gaussian, and calculated at the HF/6–31 + G* level.…”

Section: System and Methodsmentioning

confidence: 99%

Molecular dynamics simulations of ortho-carborane nano-diamond storage within the nonpolar channel cavities of a right-handed coiled-coil tetrabrachion nanotube

Harder-Viddal

Heide

Roshko

et al. 2021

Computational and Structural Biotechnology Journal

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Graphical abstract Molecular dynamics simulations have been performed on a complex in which clusters of boron in the form of molecules of the nanodiamond ortho-carborane have been inserted into the four large nonpolar cavities of a nanotube of the right-handed coiled-coil RHCC. The techniques of multi-configurational thermodynamic integration, steered molecular dynamics and umbrella sampling have been combined to investigate the energetics of storage of ortho-carborane in the cavities and to map out the free energy landscape of the complex along the central channel and along directions transverse to the central channel. The purpose of the study was to explore potential pathways for the diffusion of ortho-carborane between the cavities and the solvent and to assess the stability of the complex as a possible drug delivery system for boron neutron capture therapy (BNCT). The investigation reveals a complex free energy landscape with a multitude of peaks and valleys, all of which can be related to specific architectural elements of the , and the activation barriers for ortho-carborane capture and release support the requirements for rapid cargo uptake coupled with tight binding to the cavities.

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The MM3 force field for 12-vertex boranes and carboranes

Cited by 26 publications

References 24 publications

Tungsten carbonyl σ-complexes with charge-compensated nido-carboranyl thioether ligands

Tungsten carbonyl σ-complexes with charge-compensated nido-carboranyl thioether ligands

Molecular dynamics simulations of ortho-carborane nano-diamond storage within the nonpolar channel cavities of a right-handed coiled-coil tetrabrachion nanotube

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