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In view of the fact that the phosphorus atom in its low co-ordination state (coordination numbers 1 and 2) has been termed as the carbon copy, there have been attempts to investigate, theoretically as well as experimentally, the effect of the exchange(s) of CH- moiety with phosphorus atom(s) (CH/P) on the structural and other aspects of the classical carbocyclic and heterocyclic systems. Tropylium ion is a well-known non-benzenoid aromatic system and has been studied extensively for its aromatic character. We have now investigated the effect of mono- and poly-CH/P exchange(s) on the aromaticity of the tropylium ion. For this purpose, the parameters based on the geometry and magnetic properties, namely bond equalization, aromatic stabilization energies (ASE), Nucleus-Independent Chemical Shift (NICS) values, (NICS(0), NICS(1), NICS(1)zz), proton nucleus magnetic resonance (1H-NMR) chemical shifts, magnetic susceptibility exaltation and magnetic anisotropic values of mono-, di-, tri- and tetra-phosphatropylium ions have been determined at the Density Functional Theory (DFT) (B3LYP/6-31+G(d)) level. Geometry optimization reveals bond length equalization. ASEs range from -46.3 kcal/mol to -6.2 kcal/mol in mono- and diphospha-analogues which are planar. However, the ions having three and four phosphorus atoms lose planarity and their ASE values approach the values typical for non-aromatic structures. Of the three NICS values, the NICS(1)zz is consistently negative showing aromatic character of all the systems studied. It is also supported by the magnetic susceptibility exaltations and magnetic anisotropic values. Furthermore, 1H-NMR chemical shifts also fall in the aromatic region. The conclusion that mono-, di-, tri- and tetra-phosphatropylium ions are aromatic in nature has been further corroborated by determining the energy gap between the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) (HOMO - LUMO gap), which falls in the range, ca. 3 × 10-19-9 × 10-19 J. The systems having more than four phosphorus atoms are not able to sustain their monocyclic structure. [ABSTRACT FROM AUTHOR]

Phosphaalkenes (RP=CR 2) and diphosphenes (RP=PR) are main group analogues of alkenes (R2C=CR 2). Molecules featuring such multiply bonded phosphorus functionalities often display structural features and chemical reactivities that mimic their purely organic counterparts, lending credence to the claim that these compounds are "carbon copies". We have been expanding this analogy to include oligomers and polymers with extended conjugation that directly involve P=C and P=P units. Many of these materials, however, display little or no photoluminescence (PL). This article summarizes our efforts to understand P=C and P=P photobehavior and to produce materials having significant PL that mimic or "photocopy" the PL properties of the phosphorus-free systems. Recent materials based on benz - oxaphospholes (BOPs), benzobisoxaphospholes (BBOPs), and higher analogues having significant fluorescence quantum yields are covered. [ABSTRACT FROM AUTHOR]

The vast non-coding portion of the human genome is full of functional elements and disease-causing regulatory variants. The principles defining the relationships between these elements and distal target genes remain unknown. Promoters and distal elements can engage in looping interactions that have been implicated in gene regulation. Here we have applied chromosome conformation capture carbon copy (5C) to interrogate comprehensively interactions between transcription start sites (TSSs) and distal elements in 1% of the human genome representing the ENCODE pilot project regions. 5C maps were generated for GM12878, K562 and HeLa-S3 cells and results were integrated with data from the ENCODE consortium. In each cell line we discovered >1,000 long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites. We observed significant correlations between gene expression, promoter-enhancer interactions and the presence of enhancer RNAs. Long-range interactions show marked asymmetry with a bias for interactions with elements located ?120 kilobases upstream of the TSS. Long-range interactions are often not blocked by sites bound by CTCF and cohesin, indicating that many of these sites do not demarcate physically insulated gene domains. Furthermore, only ?7% of looping interactions are with the nearest gene, indicating that genomic proximity is not a simple predictor for long-range interactions. Finally, promoters and distal elements are engaged in multiple long-range interactions to form complex networks. Our results start to place genes and regulatory elements in three-dimensional context, revealing their functional relationships. [ABSTRACT FROM AUTHOR]