An ab initio study of the complexes formed by hypohalous acids (HOX, X = F, Cl and Br) with formaldehyde has been carried out at the MP2/aug-cc-pVTZ computational level. Two minima complexes are found, one with an H...O contact and the other one with an X...O contact. The former is more stable than the latter, and the strength difference between them decreases as the size of the X atom increases. The associated HO and XO bonds undergo a bond lengthening and red shift, whereas a blue shift was observed in the bond of the hypohalous acid not involved in the interaction. The interaction strength and properties in both complexes are analyzed with atoms in molecules (AIM) and natural bond orbital (NBO) theories. The energy decomposition analyses indicate that the contribution from the electrostatic interaction energy is larger in the hydrogen-bonded complexes than that in the halogen-bonded complexes.

The properties and applications of halogen bonds are dependent greatly on their strength. In this paper, we suggested some measures for enhancing the strength of the halogen bond relative to the hydrogen bond in the H(2)CS-HOX (X = F, Cl, and Br) system by means of quantum chemical calculations. It has been shown that with comparison to H(2)CO, the S electron donor in H(2)CS results in a smaller difference in strength for the Cl halogen bond and the corresponding hydrogen bond, and the Br halogen bond is even stronger than the hydrogen bond. The Li atom in LiHCS and methyl group in MeHCS cause an increase in the strength of halogen bonding and hydrogen bonding, but the former makes the halogen bond stronger and the latter makes the hydrogen bond stronger. In solvents, the halogen bond in the Br system is strong enough to compete with the hydrogen bond. The interaction nature and properties in these complexes have been analyzed with the natural bond orbital theory.

The main limiting factor in spatial resolution of localization microscopy is the number of detected photons. Recently we showed that cryogenic measurements improve the photostability of fluorophores, giving access to Angstrom precision in localization of single molecules. Here, we extend this method to colocalize two fluorophores attached to well-defined positions of a double-stranded DNA. By measuring the separations of the fluorophore pairs prepared at different design positions, we verify the feasibility of cryogenic distance measurement with sub-nanometer accuracy. We discuss the important challenges of our method as well as its potential for further improvement and various applications.

Rotaviruses are the single most common cause of fatal and severe childhood diarrheal illness worldwide (>125 million cases annually). Rotavirus shares structural and functional features with many viruses, such as the presence of segmented double-stranded RNA genomes selectively and tightly packed with a conserved number of transcription complexes in icosahedral capsids. Nascent transcripts exit the capsid through 12 channels, but it is unknown whether these channels specialize in specific transcripts or simply act as general exit conduits; a detailed description of this process is needed for understanding viral replication and genomic organization. To this end, we developed a single molecule assay for capturing and identifying transcripts extruded from transcriptionally active viral particles. Our findings support a model in which each channel specializes in extruding transcripts of a specific segment that in turn is linked to a single transcription complex. Our approach can be extended to study other viruses and transcription systems. ouble-stranded RNA (dsRNA) viruses comprise a wide variety of families that vary in genome complexity. These families include Reoviridae with 10-12 genomic segments; Crysoviridae with 4 segments; Cystoviridae with 3 segments; Birnaviridae, Picobirnaviridae, and Partiviridae with 2 segments; and Totiviridae with a single genomic dsRNA. They also vary in their ability to infect diverse hosts from bacteria to humans, yet they share unique features reflecting parallels in their replication; for the Reoviridae, such features include a multicomponent capsid that crosses the host cell membrane and transcription of their dsRNA segments by capsid-attached enzymes. During cell entry, the outer layers of these viruses are lost, while their inner capsids provide a compartment for genome segments (10-12 dsRNAs). Transcript export occurs via channels at the 12 vertices of an icosahedral capsid; although crucial for establishing infection (because the transcripts act as templates for both translation and genomic dsRNA synthesis), the mechanism of transcript export is unclear. In particular, it is unknown whether the nascent transcripts are selectively released through specialized channels, and if so, what the basis of selectivity is.To address these questions, we studied rotavirus, a major cause of gastroenteritis in infants and children worldwide (1, 2), and a member of the Reoviridae family, which includes many viruses of veterinary and biomedical importance (3). Rotaviruses deliver a 70-nm-diameter double-layered particle (DLP) to host cells following entry; the outer and inner protein layers package transcription complexes (TCs), proteins VP1 (RNA-dependent RNA polymerase) and VP3 (RNA capping enzyme), and 11 dsRNA genomic segments. The outer DLP layer is made of VP6 proteins (4) arranged as pentamers and hexamers forming 132 channels of three classes, including a class of 12 channels, each placed at the fivefold vertices of the icosahedral capsid. Underneath the VP6 layer is the single-lay...

Quantum chemical calculations have been performed to study the interaction of H(3)NBH(3) with dihalogen molecules XY (XY = ClF, ClCl, BrF, BrCl, and BrBr) at the MP2/aug-cc-pVTZ level. It is shown that a halogen-hydride halogen bond is formed between the two molecules, in which the sigma electron of the B-H bond in H(3)NBH(3) acts as the electron donor. The strength of the halogen bond ranges from 14.82 kJ/mol in H(3)NBH(3)-ClCl complex to 40.13 kJ/mol in H(3)NBH(3)-BrF complex at the CCSD(T)/aug-cc-pVTZ level, which is comparable to medium strong hydrogen bonds. The B-H and X-Y bonds are elongated with a concomitance of a red shift. The analyses of natural bond orbital and atoms in molecules have been carried out to understand the nature of properties of this novel interaction. The results show that this interaction has partially covalent character.

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In this article, a new type of halogen-bonded complex YCCX...HMY (X = Cl, Br; M = Be, Mg; Y = H, F, CH(3)) has been predicted and characterized at the MP2/aug-cc-pVTZ level. We named it as halogen-hydride halogen bonding. In each YCCX...HMY complex, a halogen bond is formed between the positively charged X atom and the negatively charged H atom. This new kind of halogen bond has similar characteristics to the conventional halogen bond, such as the elongation of the C-X bond and the red shift of the C-X stretch frequency upon complexation. The interaction strength of this type of halogen bond is in a range of 3.34-10.52 kJ/mol, which is smaller than that of dihydrogen bond and conventional halogen bond. The nature of the electrostatic interaction in this type of halogen bond has also been unveiled by means of the natural bond orbital, atoms in molecules, and energy decomposition analyses.

Quantum chemical calculations have been performed for the MCCBr−NCM′ (M and M′ = H, Li, Na, F, NH2, and CH3) halogen-bonded complexes at the MP2/aug-cc-pVTZ level. The binding energy is in a range of 1.34−23.42 kJ/mol. The results show that the alkali metal has a prominent effect on the strength of halogen bond, and this effect is different for the alkali metal in the halogen and electron donors. The alkali atom in the halogen donor makes it weaken greatly, whereas that in the electron donor causes it to enhance greatly. Natural bond orbital analysis shows that the alkali atom is electron-withdrawing in the halogen donor and electron-donating in the electron donor. In formation of the halogen bond, the former is a negative contribution, whereas the latter is a positive one. A similar charge transfer is also found for the H atom in the halogen and electron donors. These complexes have also been analyzed with the atoms in molecules theory.