Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate

Fan, Dingxin; Sakai, Yuki; Chelikowsky, James R.

doi:10.1103/physrevmaterials.4.053802

Cited by 9 publications

(10 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To understand interactions between the AFM tips and CO-FePc before the bond is broken, we computed frequency shifts of the probe tips at relatively large heights (z~5 Å) using optimized geometries 22 (Supplementary Figure 1). We modeled the Cu tip using a Cu 2 cluster and the CO tip using a Cu-CO cluster.…”

Section: Resultsmentioning

confidence: 99%

“…Dative bonds are commonly found in transition metal complexes and play vital roles in catalysis, organometallic chemistry, and biochemistry. Here, we focus on understanding the breaking of a single chemical bond between a CO molecule and a ferrous phthalocyanine (FePc) complex using AFM together with real-space pseudopotential density functional theory (DFT) calculations [20][21][22] . Our results reveal detailed mechanisms of bond breaking by both repulsive and attractive forces.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Breaking a dative bond with mechanical forces

et al. 2021

Self Cite

View full text Add to dashboard Cite

Bond breaking and forming are essential components of chemical reactions. Recently, the structure and formation of covalent bonds in single molecules have been studied by non-contact atomic force microscopy (AFM). Here, we report the details of a single dative bond breaking process using non-contact AFM. The dative bond between carbon monoxide and ferrous phthalocyanine was ruptured via mechanical forces applied by atomic force microscope tips; the process was quantitatively measured and characterized both experimentally and via quantum-based simulations. Our results show that the bond can be ruptured either by applying an attractive force of ~150 pN or by a repulsive force of ~220 pN with a significant contribution of shear forces, accompanied by changes of the spin state of the system. Our combined experimental and computational studies provide a deeper understanding of the chemical bond breaking process.

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Breaking a dative bond with mechanical forces

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…We then applied the Hellmann-Feynman theorem to the total ground state energies to compute the net forces acting on each atom. For the AFM image simulations, we used the same method as described in Ref [24]. (See Supplementary Materials for more details.)…”

Section: Methodsmentioning

confidence: 99%

“…Here, we report the realization of a system containing an individual CO and FePc and subsequent AFM studies of the bond rupture process under vacuum conditions, so as to minimize the effects of environmental perturbations. Together with real-space pseudopotential density functional theory (DFT) calculations [22][23][24] modeling the events, this work advances our understanding of the origins of the measured forces in dative bond breaking.…”

Section: Introductionmentioning

confidence: 95%

Breaking a Dative Bond with Mechanical Forces

Chen

Fan

Zhang

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Bond breaking and forming is essential in every chemical reaction. Here, we report a single dative bond breaking process revealing an unprecedented level of detail using noncontact atomic force microscopy. The dative bond between carbon monoxide and ferrous phthalocyanine was ruptured via mechanical forces applied by atomic force microscope tips; the process was quantitatively measured and characterized both experimentally and via first principles quantum mechanics modeling. Our results show that the bond can be ruptured either by applying an attractive force of ~150 pN (pulling) or by a repulsive force of ~220 pN (pushing), accompanied by changes of the spin state of the system. Our combined experimental and computational studies provide a deeper understanding of the chemical bond breaking process.

show abstract

“…A ligand attached to a microsphere trapped by Optical Tweezers can be brought into contact with ligands on the cell surface (also trapped by Optical Tweezers) in order to study receptor-ligand binding. In this dual trapping manner, a number of adhesion quantities like binding force, adhesion probably (the likelihood of cell-ligand binding) and steric effects (factors that affect orientation of molecules) can be [20]. Similar studies can be done in T-cell receptor binding.…”

Section: Optical Trapping -Optical Tweezersmentioning

confidence: 99%

T-Cell Receptor Clustering Methods Used for Single Cell Analysis: Potential Application in Oncology

Buttigieg¹,

Helmerson²,

Coventry³

2021

COR

View full text Add to dashboard Cite

We know that T-cell activation and effector function is integral for cancer cell destruction in immunotherapeutic treatment in oncology. The fundamental behaviour of T-cells at the time of activation is poorly understood but is likely to be central to this action. Cellular clustering occurs on at least two levels: gathering of multiple mobile cells of similar type, and aggregation between different cell types. Receptors are implicated in both of these processes. Analysis of receptor clustering is a different process whereby receptors form clusters on the cell membrane surface and can be studied to determine their relationship to immune activation. Receptor clustering has been shown to occur in some (perhaps all) cell types, but little is known about this phenomenon, particularly in T-lymphocytes. T-Cell Receptors (TCRs) which are important for the activation of T-lymphocytes. T-cell receptors, also known as cluster of differentiation 3 (CD3) molecules, bind specific antigen to create intracellular signaling in the process of T-cell activation as part of the immune response. The detail of how TCRs physically behave on the T-lymphocyte surface and specifically how they cluster remains unclear, including during the early phases of initiation of immune activation in the T-cell response. The aim of this review is to investigate how receptor clustering that has been studied, can be more effectively studied in the future and what the current evidence suggests about TCR clustering/T-cell activity relationships.

show abstract

Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate

Cited by 9 publications

References 71 publications

Breaking a dative bond with mechanical forces

Breaking a dative bond with mechanical forces

Breaking a Dative Bond with Mechanical Forces

T-Cell Receptor Clustering Methods Used for Single Cell Analysis: Potential Application in Oncology

Contact Info

Product

Resources

About