One-pot synthesis of highly luminescent carbon quantum dots and their nontoxic ingestion by zebrafish for in vivo imaging.

Photoluminescent carbon and/or silicon-based nanodots have attracted ever increasing interest. Accordingly, a myriad of synthetic methodologies have been developed to fabricate them, which unfortunately, however, frequently involve relatively tedious steps, such as initial surface passivation and subsequent functionalization. Herein, we describe a green and sustainable synthetic strategy to combine these procedures into one step and to produce highly luminescent carbon quantum dots (CQDs), which can also be easily fabricated into flexible thin films with intense luminescence for future roll-to-roll manufacturing of optoelectronic devices. The as-synthesized CQDs exhibited enhanced cellular permeability and low or even noncytotoxicity for cellular applications, as corroborated by confocal fluorescence imaging of HeLa cells as well as cell viability measurements. Most strikingly, zebrafish were directly fed with CQDs for in vivo imaging, and mortality and morphologic analysis indicated ingestion of the CQDs posed no harm to the living organisms. Hence, the multifunctional CQDs potentially provide a rich pool of tools for optoelectronic and biomedical applications.

Ear decomposition of 3-regular polyhedral links with applications.

In this paper, we introduce a notion of ear decomposition of 3-regular polyhedral links based on the ear decomposition of the 3-regular polyhedral graphs. As a result, we obtain an upper bound for the braid index of 3-regular polyhedral links. Our results may be used to characterize and analyze the structure and complexity of protein polyhedra and entanglement in biopolymers.

Quantification of hyperconjugative effect on the proton donor X-H bond length changes in the red- and blueshifted hydrogen-bonded complexes.

A whole dataset containing 55 hydrogen bonds were studied at the MP2/aug-cc-pVTZ level of theory. The changes of geometries and stretching vibrational frequencies show that there are 31 redshifted and 24 blueshifted hydrogen-bonded complexes. Natural bond orbital analysis was carried out at the B3LYP/aug-cc-pVTZ level of theory to obtain the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond, which are closely associated with its bond length. Based on their relationship, a generally applicable method considering both the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond has been developed to quantitatively describe the hyperconjugative effect on the X-H bond length changes in these hydrogen-bonded complexes.

Halogen as halogen-bonding donor and hydrogen-bonding acceptor simultaneously in ring-shaped H3N·X(Y)·HF (X = Cl, Br and Y = F, Cl, Br) complexes.

A series of ring-shaped molecular complexes formed by H(3)N, HF and XY (X = Cl, Br and Y = F, Cl, Br) have been investigated at the MP2/aug-cc-pVTZ level of theory. Their optimized geometry, stretching mode, and interaction energy have been obtained. We found that each complex possesses two red-shifted hydrogen bonds and one red-shifted halogen bond, and the two hydrogen bonds exhibit strong cooperative effects on the halogen bond. The cooperativity among the NH(3)···FH, FH···XY and H(3)N···XY interactions leads to the formations of these complexes. The AIM analysis has been performed at the CCSD(T)/aug-cc-pVQZ level of theory to examine the topological characteristics at the bond critical point and at the ring critical point, confirming the coexistence of the two hydrogen bonds and one halogen bond for each complex. The NBO analysis carried out at the B3LYP/aug-cc-pVTZ level of theory demonstrates the effects of hyperconjugation, hybridization, and polarization coming into play during the hydrogen and halogen bonding formations processes, based on which a clockwise loop of charge transfer was discovered. The molecular electrostatic potential has been employed to explore the formation mechanisms of these molecular complexes.

Topological analysis of enzymatic actions on DNA polyhedral links.

Current synthetic biology has witnessed a revolution that natural DNA molecule steps onto a broad scientific area by assembling a large variety of three-dimensional structures with the connectivity of polyhedra. A mathematical model of these biomolecules is crucial to clarify the biological self-assembly principle, and unravel a first-step understanding of biological regulation and controlling mechanisms. In this paper, mechanisms of two different enzymatic actions on DNA polyhedra are elucidated through theoretical models of polyhedral links: (1) topoisomerase that untangles DNA polyhedral links produces separated single-stranded DNA circles through the crossing change operation; (2) recombinase generates a class of polyhedral circular paths or polyhedral knots by applying the crossing smoothing operation. Furthermore, we also discuss the possibility of applying two theoretical operations in molecular design of DNA polyhedra. Thus, our research provides a new sight of how geometry and topology of DNA polyhedra can be manipulated and controlled by enzymes, as well as has implications for molecular design and structural analysis of structural genome organization.

Red- and blue-shifted hydrogen bonds in the cis-trans noncyclic formic acid dimer.

The cis-trans noncyclic formic acid dimer was studied by means of MP2 method with 6-31G(d,p), 6-31+G(d,p) and 6-311+G(d,p) basis sets. It exhibits simultaneously red-shifted O-H...O and blue-shifted C-H...O hydrogen bonds. AIM and NBO analyses are performed at the MP2/6-31+G(d,p) level to explore their properties and origins. AIM analysis provides the evidence that the O-H bond becomes weaker and the C-H bond becomes stronger upon the hydrogen bond formations. Intermolecular and intramolecular hyperconjugations have important influence on the electron densities in the X-H (X = O, C) sigma bonding orbital and its sigma* antibonding orbital. The electron densities in the two orbitals are closely connected with the X-H (X = O, C) bond length, and they are used to quantitatively estimate the bond length variation. The larger amount of charge transfer in the red-shifted O-H...O hydrogen bond is due to its favorable H...O electron channel, whereas the H...O electron channel in the blue-shifted C-H...O hydrogen bond is weaker. Structural reorganization effects shorten the C-H bond by approximately 30% when compared to the C-H bond contraction upon the dimerization. Strikingly, it leads to a small elongation and a slight red shift of the O-H bond. Both rehybridization and repolarization result in the X-H (X = O, C) bond contraction, but their effects on the O-H bond do not hold a dominant position. The hydrogen-bonding processes go through the electrostatic attractions, van der Waals interactions, charge-transfer interactions, hydrogen-bonding interactions and electrostatic repulsions. Electrostatic attractions are of great importance on the origin of the red-shifted O-H...O hydrogen bond, especially the strong H(delta+)...O(delta-) attraction. For the blue-shifted C-H...O hydrogen bond, the considerable nucleus-nucleus repulsion between H and O atoms caused by the strong electrostatic attraction between C and O atoms is a possible reason for the C-H bond contraction and its blue shift.

Red-shifted hydrogen bonds and blue-shifted van der Waals contact in the standard Watson-Crick adenine-thymine base pair.

Standard Watson-Crick adenine-thymine (AT) base pair has been investigated by using the B3LYP functional with 6-31G(d, p) basis set, at which level of theory the geometrical characteristics of the AT base pair are the best in agreement with the experiment. It exhibits simultaneously red-shifted N-H...O and N-H...N hydrogen bonds as well as a blue-shifted C-H...O contact. AIM analysis suggests that the blue-shifted C-H...O contact exists as van der Waals interaction, and the electron density rho that reflects the strength of a bond has been used to explain the red- and blue-shifted. By means of NBO analysis, we report a method to estimate the effect of hyperconjugation quantitatively, which combines the electron density in the X-H (X = N, C) sigma bonding orbital with that in the sigma* antibonding orbital. The effect of structural reorganization on the origins of the red- and blue-shifted has been considered by the partial optimization, its behavior on the X-H (X = N, C) bond is quite different. Rehybridization and repolarization models are employed, and they act as bond-shortening effects. The competition between the electrostatic attractions and Pauli/nucleus repulsions is present in the two typical red-shifted N-H...O and N-H...N hydrogen bonds as well as in the blue-shifted C-H...O van der Waals contact. Electrostatic attraction between H and Y atoms (Y = O, N) is an important reason for the red shift, while the nucleus-nucleus repulsion between H and O atoms may be a factor leading to the C-H bond contraction and its blue shift. The electric field effect induced by the acceptor O atom on the C-H bond is also discussed.

Identification and functional characterization of a novel transglutaminase 1 gene mutation associated with autosomal recessive congenital ichthyosis.

BACKGROUND: Autosomal recessive congenital ichthyosis (ARCI) is a group of genetically heterogeneous diseases. Mutations in transglutaminase (TGase) 1 gene (TGM1, OMIM 190195) have been implicated in ARCI. However, little is known about TGM1 mutations in the Chinese population, and no functional studies have investigated the biological effect of mutant TGM1 on human epidermal keratinocytes (HaCaT) cells. OBJECTIVES: To identify the pathogenic mutations of TGM1 gene in two Chinese siblings with ARCI and gain insight into functional consequences of these mutations. METHODS: Fifteen exons and flanking splice sites of TGM1 gene were amplified by polymerase chain reaction and then underwent bidirectional Sanger sequencing. The HaCaT cells were transfected with lentiviral vectors, which overexpressed either wild-type or mutant TGM1 cDNAs with deleted homeodomain. Cell proliferation and cell cycle progression were detected. The expression of cyclin D1, cyclin B1, CDK4, TGM1, K10, involucrin, and filaggrin proteins were investigated by Western blot analysis. RESULTS: We found two compound heterozygous missense mutations (c.515C>T, R143C in exon 3 and c.759C>T, S212F in exon 4) in both siblings. HaCaT cells transfected with mutant TGM1 cDNAs displayed a lower growth rate and delayed S phase while overexpression of wild-type TGM1 cDNAs led to accelerated growth. HaCaT cells transfected with mutant TGM1 cDNAs displayed lower expression of differentiation markers such as involucrin and filaggrin. Our findings suggest that the compound heterozygous missense (c.515C>T, R143C) mutations in exon 3 and missense (c.759C>T, S212F) mutations in exon 4 result in the phenotype of ARCI. TGM1 mutations can suppress keratinocyte growth and cornified cell envelope formation.

Nicotinic acid and its derivatives: synthetic routes, crystal forms and polymorphs.

Nicotinic acid is a well-known pharmaceutical in the vitamin B group that has attracted great interest in the past decades due to its significant importance in the treatment of the human diseases like pellagra. Also, nicotinic acid derivatives have been devoted to much attention due to their different pharmaceutical effects in the treatment of diseases. In view of this, the developments of nicotinic acid and its derivatives including their synthetic methods by using different substrates, and their structural modifications (e.g., substitution of one or more positions of pyridyl ring or acid) were reviewed in details. Drug molecules like nicotinic acid and its derivatives may exist in more than one crystal form in its solid state, known as polymorphs. Different polymorphs have different dissolution rates and aqueous solubility. Therefore, we reviewed structures of different crystal forms of nicotinic acid and its derivatives.

A new Euler's formula for DNA polyhedra.

DNA polyhedra are cage-like architectures based on interlocked and interlinked DNA strands. We propose a formula which unites the basic features of these entangled structures. It is based on the transformation of the DNA polyhedral links into Seifert surfaces, which removes all knots. The numbers of components µ, of crossings c, and of Seifert circles s are related by a simple and elegant formula: s + µ = c + 2. This formula connects the topological aspects of the DNA cage to the Euler characteristic of the underlying polyhedron. It implies that Seifert circles can be used as effective topological indices to describe polyhedral links. Our study demonstrates that, the new Euler's formula provides a theoretical framework for the stereo-chemistry of DNA polyhedra, which can characterize enzymatic transformations of DNA and be used to characterize and design novel cages with higher genus.