Inhibition of vibrational energy flow within an aromatic scaffold via heavy atom effect.

The regulation of intramolecular vibrational energy redistribution (IVR) to influence energy flow within molecular scaffolds provides a way to steer fundamental processes of chemistry, such as chemical reactivity in proteins and design of molecular diodes. Using two-dimensional infrared (2D IR) spectroscopy, changes in the intensity of vibrational cross-peaks are often used to evaluate different energy transfer pathways present in small molecules. Previous 2D IR studies of para-azidobenzonitrile (PAB) demonstrated that several possible energy pathways from the N3 to the cyano-vibrational reporters were modulated by Fermi resonance, followed by energy relaxation into the solvent [Schmitz et al., J. Phys. Chem. A 123, 10571 (2019)]. In this work, the mechanisms of IVR were hindered via the introduction of a heavy atom, selenium, into the molecular scaffold. This effectively eliminated the energy transfer pathway and resulted in the dissipation of the energy into the bath and direct dipole-dipole coupling between the two vibrational reporters. Several structural variations of the aforementioned molecular scaffold were employed to assess how each interrupted the energy transfer pathways, and the evolution of 2D IR cross-peaks was measured to assess the changes in the energy flow. By eliminating the energy transfer pathways through isolation of specific vibrational transitions, through-space vibrational coupling between an azido (N3) and a selenocyanato (SeCN) probe is facilitated and observed for the first time. Thus, the rectification of this molecular circuitry is accomplished through the inhibition of energy flow using heavy atoms to suppress the anharmonic coupling and, instead, favor a vibrational coupling pathway.

Fibrous hamartoma of infancy: imaging findings.

BACKGROUND: Fibrous hamartoma of infancy is a benign tumor that typically arises within the first 2 years of life in the subcutaneous and lower dermal layers. Diagnosis can be challenging as it is a rare tumor, and the imaging appearance is not well known. OBJECTIVE: To describe the imaging features in 4 cases of fibrous hamartoma of infancy focusing on ultrasound (US) and magnetic resonance (MR) findings. MATERIALS AND METHODS: In this retrospective IRB-approved study, informed consent was waived. We searched patient charts for histopathology-confirmed fibrous hamartoma of infancy diagnosis between November 2013 and November 2022. We found four cases, three boys and one girl, and the mean age was 1.4 years (5 months-3 years). The lesions were located in the axilla, posterior elbow, posterior neck, and lower back. All four patients underwent ultrasound evaluation of the lesion, and two patients also underwent MRI evaluation. The imaging findings were reviewed by consensus by two pediatric radiologists. RESULTS: US imaging revealed subcutaneous lesions with variably defined hyperechoic regions and intervening hypoechoic bands resulting in a linear "serpentine" pattern or a "multiple semicircle" pattern. MR imaging evidenced heterogeneous soft tissue masses, localized in the subcutaneous fat, and showed hyperintense fat interspersed with hypointense septations on both T1- and T2-weighted images. CONCLUSION: Fibrous hamartoma of infancy has a suggestive appearance on US with heterogeneous, echogenic subcutaneous lesions with intervening hypoechoic portions, in parallel or circumferential arrangement that can be seen as a serpentine or semicircular pattern. On MRI, interspersed macroscopic fatty components show high signal intensity on T1- and T2-weighted images and reduced signal on fat-suppressed inversion recovery images, with irregular peripheral enhancement.

Subcutaneous fat necrosis of the newborn: a pictorial essay of an under-recognized entity.

Subcutaneous fat necrosis of the newborn is a self-limited disorder predominantly affecting full-term and post-term neonates during the first 6 weeks after birth. Subcutaneous fat necrosis can be focal or multifocal and affect one or both sides with a predilection for areas of pressure in certain anatomical areas. Subcutaneous fat necrosis of the newborn is associated with perinatal asphyxia and other neonatal and maternal risk factors. Subcutaneous fat necrosis of the newborn presents as a self-limited area of dermal edema followed by indurated subcutaneous plaques, or nontender and mobile nodules, sometimes with skin discoloration [1-3]. The diagnosis is based on the child's history and physical examination, but when in doubt, imaging is helpful. US is the imaging modality of choice to confirm the diagnosis of subcutaneous fat necrosis of the newborn because it provides the best resolution of superficial lesions, requires no sedation and lacks ionizing radiation. US can also help evaluate and characterize other pathologies affecting the superficial subcutaneous soft tissues at this age. Familiarity with subcutaneous fat necrosis of the newborn is important to make a prompt and precise diagnosis and avoid unnecessary imaging tests or invasive procedures.

Evaluation of the Viability of Untreated Leiomyomas Using Computed Tomography-Detected Calcification Patterns.

OBJECTIVE: To evaluate the relationship between computed tomography (CT)-detected calcification patterns and Magnetic Resonance Imaging (MRI) enhancement as a surrogate for viability in untreated uterine leiomyomas. METHODS: We queried 2 university hospital databases to identify patients with: (1) at least 1 calcified leiomyoma on CT greater than 1 cm (2) contrast-enhanced MRI of the pelvis performed within 5 years of the CT, and (3) no prior history of uterine fibroid embolization (UFE). Computed tomography was used to analyze calcification pattern and contrast-enhanced MRI to analyze size and viability. RESULTS: There were 12,862 reports that fit the criteria. After exclusion, 50 patients with 74 calcified untreated leiomyomas were analyzed. Three calcification patterns were identified: rim (n = 22), diffuse (n = 9), and coarse either less than or greater than 50% (n = 43). Four of 22 (18%) of leiomyomas with rim calcification were viable. Three of 9 (33%) of leiomyomas with diffuse calcification were viable. All leiomyomas with coarse calcifications were viable, 43 of 43 (100%). CONCLUSIONS: Leiomyomas with coarse calcifications are viable, whereas the majority with rim or diffuse calcification are not. This information may be helpful when triaging symptomatic women to treatment.

Normal and abnormal tendons in children: evaluation with ultrasound.

Ultrasound (US) has emerged as an essential diagnostic tool for evaluating the entire musculoskeletal system in children. The spatial resolution of modern US technology offers unparalleled depiction of superficial anatomy, and motion and blood flow are demonstrated in real time allowing for the quick diagnosis of a wide variety of pathologies. US evaluation of tendons and their structure and function represents one of the best applications of musculoskeletal US. This article reviews some of the more common indications for US of the tendons in children. While not an exhaustive list, the anatomy and pathology examples described should help any pediatric radiologist confronted with a case of tendon pain or loss of function.

Extending the vibrational lifetime of azides with heavy atoms.

The development of novel vibrational reporters (VRs), aka infrared (IR) probes, to study local environments and dynamic processes in biomolecules and materials continues to be an important area of research. Azides are important VRs because of their small size and large transition dipole strengths, however, their relatively short vibrational lifetimes (<2 ps) have limited their full potential. Herein we report that the vibrational lifetimes of azides can be increased by attaching them to heavy atoms and by using heavy 15N isotopes. Three group 14 atom triphenyl azides (Ph3CN3, Ph3SiN3, Ph3SnN3), and their triple-15N isotopomers, were synthesized in good yields. Tributyltin azide and its heavy isotopomer (Bu3Sn15N3) were also prepared to probe the effect of molecular scaffolding. The extinction coefficients for the natural abundance azides were determined, ranging from 900 to 1500 M-1 cm-1. The vibrational lifetimes of all azides were measured by pump-probe IR spectroscopy and each showed a major component with a short-to-moderate vibrational lifetime and a minor component with a much longer vibrational lifetime. Based on these results, the lifetime, aka the observation window, of an azide reporter can be extended from ∼2 ps to as long as ∼300 ps by a combination of isotopic labeling and heavy atom effect. 2D IR measurements of these compounds further confirmed the ability to observe these azide transitions at much longer timescales showing their utility to capture dynamic processes from tens to hundreds of picoseconds.

2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks.

Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035-4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.

Design and synthesis of a bis-macrocyclic host and guests as building blocks for small molecular knots.

The thread-link-cut (TLC) approach has previously shown promise as a novel method to synthesize molecular knots. The modular second-generation approach to small trefoil knots described herein involves electrostatic interactions between an electron-rich bis-macrocyclic host compound and electron-deficient guests in the threading step. The bis-macrocyclic host was synthesized in eight steps and 6.6% overall yield. Ammonium and pyridinium guests were synthesized in 4-5 steps. The TLC knot-forming sequence was carried out and produced a product with the expected molecular weight, but, unfortunately, further characterization did not produce conclusive results regarding the topology of the product.

Tuning Molecular Vibrational Energy Flow within an Aromatic Scaffold via Anharmonic Coupling.

From guiding chemical reactivity in synthesis or protein folding to the design of energy diodes, intramolecular vibrational energy redistribution harnesses the power to influence the underlying fundamental principles of chemistry. To evaluate the ability to steer these processes, the mechanism and time scales of intramolecular vibrational energy redistribution through aromatic molecular scaffolds have been assessed by utilizing two-dimensional infrared (2D IR) spectroscopy. 2D IR cross peaks reveal energy relaxation through an aromatic scaffold from the azido- to the cyano-vibrational reporters in para-azidobenzonitrile (PAB) and para-(azidomethyl)benzonitrile (PAMB) prior to energy relaxation into the solvent. The rates of energy transfer are modulated by Fermi resonances, which are apparent by the coupling cross peaks identified within the 2D IR spectrum. Theoretical vibrational mode analysis allowed the determination of the origins of the energy flow, the transfer pathway, and a direct comparison of the associated transfer rates, which were in good agreement with the experimental results. Large variations in energy-transfer rates, approximately 1.9 ps for PAB and 23 ps for PAMB, illustrate the importance of strong anharmonic coupling, i.e., Fermi resonance, on the transfer pathways. In particular, vibrational energy rectification is altered by Fermi resonances of the cyano- and azido-modes allowing control of the propensity for energy flow.

Azidoethoxyphenylalanine as a Vibrational Reporter and Click Chemistry Partner in Proteins.

An unnatural amino acid, 4-(2-azidoethoxy)-L-phenylalanine (AePhe, 1), was designed and synthesized in three steps from known compounds in 54% overall yield. The sensitivity of the IR absorption of the azide of AePhe was established by comparison of the frequency of the azide asymmetric stretch vibration in water and dimethyl sulfoxide. AePhe was successfully incorporated into superfolder green fluorescent protein (sfGFP) at the 133 and 149 sites by using the amber codon suppression method. The IR spectra of these sfGFP constructs indicated that the azide group at the 149 site was not fully solvated despite the location in sfGFP and the three-atom linker between the azido group and the aromatic ring of AePhe. An X-ray crystal structure of sfGFP-149-AePhe was solved at 1.45 Å resolution and provides an explanation for the IR data as the flexible linker adopts a conformation which partially buries the azide on the protein surface. Both sfGFP-AePhe constructs efficiently undergo a bioorthogonal strain-promoted click cycloaddition with a dibenzocyclooctyne derivative.

Profiles in chemistry: a historical perspective on the national organic symposium.

This perspective delineates the history of the National Organic Chemistry Symposium (NOS) and, in doing so, traces the development of organic chemistry over the past 88 years. The NOS is the premier event sponsored by the ACS Division of Organic Chemistry (ORGN) and has been held in odd-numbered years since 1925, with the exceptions of 1943 and 1945. During the 42 symposia, 332 chemists have given 549 plenary lectures. The role the NOS played in the launch of The Journal of Organic Chemistry and Organic Reactions and the initiation of the Roger Adams Award are discussed. Representative examples highlighting the chemistry presented in each era are described, and the evolution of the field is examined by assigning each NOS talk to one of seven subdisciplines and analyzing how the number of talks in each subdiscipline has changed over time. Comparisons of the demographics of speakers, attendees, and ORGN members are made, and superlatives are noted. Personal interest stories of the speakers are discussed, along with the relationships among them, especially their academic lineage. Logistical aspects of the NOS and their historical trends are reviewed. Finally, the human side of science is examined, where over the past century, the NOS has been intertwined with some of the most heated debates in organic chemistry. Conflicts and controversies involving free radicals, reaction mechanisms, and nonclassical carbocations are discussed.

Pericardial lymphangioma: a rare benign albeit variably symptomatic tumefactive lesion.

Primary pericardial-based tumefactive lesions include pericardial cysts, mature teratomas, and lymphangiomas, and while benign they may result in clinical symptomatology that leads to their radiologic detection. We present the case of a 5-year-old boy with a heart murmur who was otherwise healthy and without significant medical history. Transthoracic echocardiogram, computed tomography, and magnetic resonance imaging studies revealed a pericardial multicystic mass imparting compression upon the right atrium and ventricle. The case proceeded to surgery in which complete resection of the mass was performed without complication, and the patient was discharged three days after. Pathology examination of the lesion determined it to be a pericardial lymphangioma with characteristic histologic features of sequestered vascular channels lined by endothelium that specifically expressed lymphatic-specific podoplanin (also known as D2-40), and with associated adipose tissue, smooth muscle bundles, and reactive lymphoid aggregates. Although a rare underlying etiology for mediastinal and specifically pericardial tumors, lymphangiomas should be considered in the differential of tumefactive lesions in this anatomic location.

Unraveling Complex Local Protein Environments with 4-Cyano-l-phenylalanine.

We present a multifaceted approach to effectively probe complex local protein environments utilizing the vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNPhe) in the model system superfolder green fluorescent protein (sfGFP). This approach combines temperature-dependent infrared (IR) spectroscopy, X-ray crystallography, and molecular dynamics (MD) simulations to provide a molecular interpretation of the local environment of the nitrile group in the protein. Specifically, a two-step enantioselective synthesis was developed that provided an 87% overall yield of pCNPhe in high purity without the need for chromatography. It was then genetically incorporated individually at three unique sites (74, 133, and 149) in sfGFP to probe these local protein environments. The incorporation of the UAA site-specifically in sfGFP utilized an engineered, orthogonal tRNA synthetase in E. coli using the Amber codon suppression protocol, and the resulting UAA-containing sfGFP constructs were then explored with this approach. This methodology was effectively utilized to further probe the local environments of two surface sites (sites 133 and 149) that we previously explored with room temperature IR spectroscopy and X-ray crystallography and a new interior site (site 74) featuring a complex local environment around the nitrile group of pCNPhe. Site 133 was found to be solvent-exposed, while site 149 was partially buried. Site 74 was found to consist of three distinct local environments around the nitrile group including nonspecific van der Waals interactions, hydrogen-bonding to a structural water, and hydrogen-bonding to a histidine side chain.

A direct comparison of azide and nitrile vibrational probes.

The synthesis of 2'-azido-5-cyano-2'-deoxyuridine, N(3)CNdU (1), from trityl-protected 2'-amino-2'-deoxyuridine was accomplished in four steps with a 12.5% overall yield. The IR absorption positions and profiles of the azide and nitrile group of N(3)CNdU were investigated in 14 different solvents and water/DMSO solvent mixtures. The azide probe was superior to the nitrile probe in terms of its extinction coefficient, which is 2-4 times larger. However, the nitrile IR absorbance profile is generally less complicated by accidental Fermi resonance. The IR frequencies of both probes undergo a substantial red shift upon going from water to aprotic solvents such as THF or DMSO. DFT calculations supported the hypothesis that the molecular origin of the higher observed frequency in water is primarily due to hydrogen bonds between the probes and water molecules.

2D IR photon echo of azido-probes for biomolecular dynamics.

The vibrations in the azido-, N(3), asymmetric stretching region of 2'-azido-2'-deoxyuridine (N(3)dU) are examined by two-dimensional infrared spectroscopy. In water and tetrahydrofuran (THF), the spectra display a single sharp diagonal peak that shows solvent sensitivity. The frequency-frequency correlation time in water is 1.5 ps, consistent with H-bond making and breaking dynamics. The 2D IR spectrum is reproduced for N(3)dU in water based on a model correlation function and known linear response functions. Its large extinction coefficient, vibrational frequency outside the protein and nucleic acid IR absorption, and sensitivity to water dynamics render -N(3) a very useful probe for 2D IR and other nonlinear IR studies: its signal is ca. 100 times that of nitriles.

CTA utilization for evaluation of suspected pulmonary embolism in a tertiary pediatric emergency department.

OBJECTIVE: To evaluate changes in the utilization of computed tomography angiography (CTA) for evaluating suspected pulmonary embolism (PE) and the positive rate of ancillary for those studies negative for PE in the last 13 years. MATERIALS AND METHODS: A retrospective review of patient ≤ 20 years of age who underwent a chest CT angiography to rule out PE was performed in a 13-year-period. CT angiographies were grouped into three categories: Positive for PE, negative for PE and positive for ancillary findings, and negative for any pathology. From the exams with ancillary findings, we examined how many of these had a chest radiograph perform within 24 h prior to the CTA and how many of them had an impression stating the same conclusion as the CTA. RESULTS: 307 chest CT angiographies for suspected PE were included. 50 (16%) were reported as positive for PE and 91 (30%) were negative for PE but positive for ancillary findings. The most frequent ancillary findings were pneumonia (n = 26) and pleural effusion (n = 11). Out of 91, 73 patients had a previous chest radiograph and 28 of them reported a similar diagnosis than the CTA. The number of CT angiographies indicated for PE increased by 3.2 studies per year. The rate of CT angiographies positive for ancillary findings (slope = 1.5) and positive for PE (slope = 0.3) remained similar throughout the same period. CONCLUSIONS: CTA orders for PE have been increasing without any increased detection of PE or ancillary findings in children.

Paired Spectroscopic and Crystallographic Studies of Proteases.

The active sites of subtilisin and trypsin have been studied by paired IR spectroscopic and X-ray crystallographic studies. The active site serines of the proteases were reacted with 4-cyanobenzenesulfonyl fluoride (CBSF), an inhibitor that contains a nitrile vibrational reporter. The nitrile stretch vibration of the water-soluble inhibitor model, potassium 4-cyanobenzenesulfonate (KCBSO), and the inhibitor were calibrated by IR solvent studies in H2O/DMSO and the frequency-temperature line-slope (FTLS) method in H2O and THF. The inhibitor complexes were examined by FTLS and the slopes of the best fit lines for subtilisin-CBS and trypsin-CBS in aqueous buffer were both measured to be -3.5×10-2 cm-1/°C. These slopes were intermediate in value between that of KCBSO in aqueous buffer and CBSF in THF, which suggests that the active-site nitriles in both proteases are mostly solvated. The X-ray crystal structures of the subtilisin-CBS and trypsin-CBS complexes were solved at 1.27 and 1.32 Å, respectively. The inhibitor was modelled in two conformations in subtilisin-CBS and in one conformation in the trypsin-CBS. The crystallographic data support the FTLS data that the active-site nitrile groups are mostly solvated and participate in hydrogen bonds with water molecules. The combination of IR spectroscopy utilizing vibrational reporters paired with X-ray crystallography provides a powerful approach to studying protein structure.

A vibrational probe for local nucleic acid environments: 5-cyano-2'-deoxyuridine.

Nitriles have been shown to be effective vibrational probes of local environments in proteins but have yet to be fully utilized for the study of nucleic acids. The potential utility of 5-cyano-2'-deoxyuridine ( 1) as a probe of local nucleic acid environment was investigated by measuring the dependence of the IR nitrile stretching frequency (nu CN), line shape, and absorbance on solvent and temperature. The nu CN was found to be sensitive to solvent with an observed blue shift of 9.2 cm (-1) in going from THF to water. The dependence of the nitrile IR absorbance band was further investigated in water-THF mixtures. Global line shape analysis, difference FTIR spectroscopy, and singular value decomposition (SVD) were used to show the presence of three distinct local environments around the nitrile group of 1 in these mixtures. A modest blue shift in nu CN was observed upon a hydrogen-bond-mediated heterodimer formation between 2 (a silyl ether analogue of 1) and 2,6-diheptanamido-pyridine ( 3a) in chloroform. The intrinsic temperature dependence of the nu CN was found to be minimal and linear over the temperature range studied. The experimental studies were complemented by density functional theory (DFT) calculations on the dependence of the nitrile stretching frequency on solute-solvent interactions and upon heterodimer formation with model systems.

Vibrational stark effect probes for nucleic acids.

The vibrational Stark effect (VSE) has proven to be an effective method for the study of electric fields in proteins via the use of infrared probes. To explore the use of VSE in nucleic acids, we investigated the Stark spectroscopy of nine structurally diverse nucleosides. These nucleosides contained nitrile or azide probes in positions that correspond to both the major and minor grooves of DNA. The nitrile probes showed better characteristics and exhibited absorption frequencies over a broad range; that is, from 2253 cm-1 for 2'-O-cyanoethyl ribonucleosides 8 and 9 to 2102 cm(-1) for a 13C-labeled 5-thiocyanatomethyl-2'-deoxyuridine 3c. The largest Stark tuning rate observed was |Deltamu| = 1.1 cm(-1)/(MV/cm) for both 5-cyano-2'-deoxyuridine 1 and N2-nitrile-2'-deoxyguanosine 7. The latter is a particularly attractive probe because of its high extinction coefficient (epsilon = 412 M-1cm-1) and ease of incorporation into oligomers.

Synthesis and Evaluation of the Sensitivity and Vibrational Lifetimes of Thiocyanate and Selenocyanate Infrared Reporters.

Two novel 2'-deoxyadenosine (dA) analogues, Si2-dA-SCN and Si2-dA-SeCN, and two novel phenylalanine (Phe) analogues, Boc-Me-PheCH2SCN and Boc-Me-PheCH2SeCN, have been synthesized and the thiocyanate (SCN) and selenocyanate (SeCN) functional groups evaluated as vibrational reporters. The syntheses of Si2-dA-SCN and Si2-dA-SeCN were accomplished in three steps in 16% and 32% overall yields, respectively, and the syntheses of Boc-Me-PheCH2SCN and Boc-Me-PheCH2SeCN were completed in four steps in 8.9% and 2.3% overall yields, respectively. The SCN and SeCN stretch vibrational modes were shown to be sensitive to the local environment by frequency shifts and full-width half-maximum (fwhm) changes in response to tetrahydrofuran (THF) and THF/water solvent mixtures. The vibrational lifetimes of the Si2-dA-SeCN (237±12 ps) and Boc-Me-PheCH2SeCN (295±31 ps) in THF solution were determined by ultrafast infrared pump-probe spectroscopy to be 1.5 to 3 times longer than those for Si2-dA-SCN (140±6 ps) and Boc-Me-PheCH2SCN (102±4 ps). The longer lifetimes for the SeCN analogues were attributed to the better insulating effects of the heavier selenium atom compared to the sulfur atom. The solvent sensitivity and longer vibrational lifetimes compared to other vibrational reporters suggest that SCN and SeCN vibrational reporters are well suited to studying several dynamic processes including protein and nucleic acid hydration and conformational changes, however stability issues may require post-synthetic modification methods to incorporate these reporters into biomacromolecules.