Abstract:The adsorption and surface reactions of ICN, BrCN, and ClCN on the Si(100)-(2×1) surface are studied using ab initio quantum calculations on single-and triple-dimer silicon clusters. These cyanogen halides can physisorb into an end-on molecular species that is bound through the N to the Si cluster via a dative bond. The adsorption energy of this dative bonded species is found to depend on the cluster size. This species can further react to form a side-on intermediate by reacting across the Si-dimer bond or can… Show more
“…A single-dimer cluster has been previously utilized to model the adsorption and decomposition of XCN. 12,13 Although the lowest energy reaction product, an adsorbed atomic halide and a molecular CN group, is in agreement with experimental results, 10,11 the activation energies computed along the single-dimer pathways suggest that at least one intermediate structure should have been observed. One possible explanation is that additional reaction pathways with multiple Si-dimers clusters can provide alternative decomposition pathways with lower activations energies than those found in the single-dimer studies.…”
Section: Introductionsupporting
confidence: 82%
“…Upon annealing to room temperature, the XC bond of the molecularly adsorbed XCN species dissociates and the adsorbed species rearranges to form a CN group bound through the C atom and an adsorbed Cl atom. A single-dimer cluster has been previously utilized to model the adsorption and decomposition of XCN. , Although the lowest energy reaction product, an adsorbed atomic halide and a molecular CN group, is in agreement with experimental results, , the activation energies computed along the single-dimer pathways suggest that at least one intermediate structure should have been observed.…”
Section: Introductionsupporting
confidence: 55%
“…10,11 Kadossov et al have previously investigated the adsorption and decomposition of ClCN, BrCN, and ICN using single-dimer models. 12,13 However, the large transition state barrier of TS3 for the dissociation of the CCl bond on the single-dimer clusters raised questions as to why none of the intermediates, for example the bridged ClCN2 species, were observed in the experiment. To complicate matters further, the TS3 transition state on larger multiple Si-dimer models could not be found with only one imaginary frequency or without constraints.…”
Electronic structure calculations for ClCN adsorbed multiple Si-dimer clusters are performed to investigate dissociation pathways for ClCN into adsorbed atomic Cl and molecular CN. Reaction pathways across adjacent Si-dimers are modeled using double-dimer (Si15H16) and triple-dimer (Si21H20) clusters. Clusters created by combining two single-dimer (Si23H24), double-dimer (Si39H32), or triple-dimer (Si55H40) clusters in an end-to-end fashion are utilized to investigate pathways across two Si-dimer rows. These computations show that the key step in the decomposition of ClCN on the Si(100) surface is the dissociation of the CCl bond. The CCl bond dissociation across two Si-dimers either in the same row or in different rows is significantly lower than that found for dissociation across a single Si-dimer. The use of multiple-dimer reaction pathways is required to provide a realistic model for ClCN dissociation on the Si(100) surface. These computations provide an explanation for the experimental observation of only the adsorbed ClCN species and final adsorbed atomic Cl and molecular CN species on the Si(100) surface.
“…A single-dimer cluster has been previously utilized to model the adsorption and decomposition of XCN. 12,13 Although the lowest energy reaction product, an adsorbed atomic halide and a molecular CN group, is in agreement with experimental results, 10,11 the activation energies computed along the single-dimer pathways suggest that at least one intermediate structure should have been observed. One possible explanation is that additional reaction pathways with multiple Si-dimers clusters can provide alternative decomposition pathways with lower activations energies than those found in the single-dimer studies.…”
Section: Introductionsupporting
confidence: 82%
“…Upon annealing to room temperature, the XC bond of the molecularly adsorbed XCN species dissociates and the adsorbed species rearranges to form a CN group bound through the C atom and an adsorbed Cl atom. A single-dimer cluster has been previously utilized to model the adsorption and decomposition of XCN. , Although the lowest energy reaction product, an adsorbed atomic halide and a molecular CN group, is in agreement with experimental results, , the activation energies computed along the single-dimer pathways suggest that at least one intermediate structure should have been observed.…”
Section: Introductionsupporting
confidence: 55%
“…10,11 Kadossov et al have previously investigated the adsorption and decomposition of ClCN, BrCN, and ICN using single-dimer models. 12,13 However, the large transition state barrier of TS3 for the dissociation of the CCl bond on the single-dimer clusters raised questions as to why none of the intermediates, for example the bridged ClCN2 species, were observed in the experiment. To complicate matters further, the TS3 transition state on larger multiple Si-dimer models could not be found with only one imaginary frequency or without constraints.…”
Electronic structure calculations for ClCN adsorbed multiple Si-dimer clusters are performed to investigate dissociation pathways for ClCN into adsorbed atomic Cl and molecular CN. Reaction pathways across adjacent Si-dimers are modeled using double-dimer (Si15H16) and triple-dimer (Si21H20) clusters. Clusters created by combining two single-dimer (Si23H24), double-dimer (Si39H32), or triple-dimer (Si55H40) clusters in an end-to-end fashion are utilized to investigate pathways across two Si-dimer rows. These computations show that the key step in the decomposition of ClCN on the Si(100) surface is the dissociation of the CCl bond. The CCl bond dissociation across two Si-dimers either in the same row or in different rows is significantly lower than that found for dissociation across a single Si-dimer. The use of multiple-dimer reaction pathways is required to provide a realistic model for ClCN dissociation on the Si(100) surface. These computations provide an explanation for the experimental observation of only the adsorbed ClCN species and final adsorbed atomic Cl and molecular CN species on the Si(100) surface.
“…The n(O) → σ*(N‘−P) interaction (Figure ) is a generalized anomeric interaction of the Lp−X−A−Y variety where “Lp” represents a lone pair, “X”, any heteroatom, “A” an electropositive atom, and “Y” and electronegative atom. ,,, The generalized anomeric effect has been well documented as being responsible for a wide variety of effects most notably in molecular conformation. − 8 Schematic and orbital diagram of the anomeric interaction in 3a between n(O) and σ*(N‘−P).…”
Section: Resultsmentioning
confidence: 99%
“…70,71,84,85 The generalized anomeric effect has been well documented as being responsible for a wide variety of effects most notably in molecular conformation. [86][87][88] The computations provide an explanation on why increased phosphoryl protonation results in shorter N′-P bonds. A phosphoryl group has three lone pairs on each of the two negatively charged oxygen atoms and two lone pairs on the neutral oxygen atom (Figure 8).…”
Electronic structure calculations have been performed on a model N-phosphorylguanidine, or phosphagen, to understand the stereoelectronic factors contributing to the lability of the "high-energy" N-P bond. The lability of the N-P bond is central to the physiological role of phosphagens involving phosphoryl transfer reactions important in cellular energy buffering and metabolism. Eight protonated forms of N-methyl-N'-phosphorylguanidine have been energy minimized at levels of theory ranging up to B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) to investigate the correlation between protonation state and N-P bond length. Selected forms have also been minimized using the CCSD/6-311++G(d,p) and QCISD/6-311++G(d,p) levels of theory. Bulk solvation energies using the polarized continuum model (PCM) with B3LYP/6-311++G(d,p) test the influence of the surroundings on computed structures and energies. The N-P bond length depends on the overall protonation state where increased protonation at the phosphoryl group or deprotonation at the unsubstituted N'' nitrogen results in shorter, stronger N-P bonds. Natural bond orbital analysis shows that the protonation state affects the N-P bond length by altering the magnitude of stabilizing n(O) --> sigma*(N-P) stereoelectronic interactions and to a lesser extent the sigma(N-P) --> sigma*(C-N'') and sigma(N-P) --> sigma*(C-N) interactions. The computations do not provide evidence of a competition between the phosphoryl and guanidinium groups for the same lone pair on the bridging nitrogen, as previously suggested by opposing resonance theory. The computed n(O) --> sigma*(N-P) anomeric effect provides a novel explanation of "high-energy" N-P bond lability. This offers new mechanistic insight into phosphoryl transfer reactions involving both phosphagens and other biochemically important "high-energy" phosphoester bonds.
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