Unveiling the reactivity of truxillic and truxinic acids (TXAs): deprotonation, anion center dot center dot center dot HO, cation center dot center dot center dot O and cation center dot center dot center dot pi interactions in TXA (0) center dot center dot center dot Y+ and TXA (0) center dot center dot center dot Z (-) complexes (Y= Li, Na, K; Z= F, Cl, Br)
- Isamura, Bienfait K, Patouossa, Issofa, Muya, Jules T, Lobb, Kevin A
- Authors: Isamura, Bienfait K , Patouossa, Issofa , Muya, Jules T , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452827 , vital:75173 , xlink:href="https://link.springer.com/content/pdf/10.1007/s11224-022-01965-5.pdf"
- Description: Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0 , and Y+ (Y=Li, Na, K) and Z− (Z=F, Cl, Br) ions using M06-2X, B3LYP and 휔 B97XD functionals in conjunction with the 6–31+ +G(d,p), aug-cc-pVDZ(-X2C) and 6–311+ +G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation…O and cation-π interactions, while Z− anions generally establish anion… H–O contacts. Predicted binding energies at the M06-2X/6–311+ +G(d,p) level range between−26.6 and−70.2 kcal/mol for cationic complexes and−20.4 and−62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O…cation…O interactions where the cation is trapped between O37 and O38 atoms of TXA0 . Anions do not behave uniformly towards TXA0 : while the fuoride anion F− induces the deprotonation of TXA0 , Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0 …Y+ and TXA0 …Z− complexes are mainly stabilized by electrostatic and inductive efects, whose combined contributions account for more than 60 percent of the total interaction energy.
- Full Text:
- Date Issued: 2023
- Authors: Isamura, Bienfait K , Patouossa, Issofa , Muya, Jules T , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452827 , vital:75173 , xlink:href="https://link.springer.com/content/pdf/10.1007/s11224-022-01965-5.pdf"
- Description: Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0 , and Y+ (Y=Li, Na, K) and Z− (Z=F, Cl, Br) ions using M06-2X, B3LYP and 휔 B97XD functionals in conjunction with the 6–31+ +G(d,p), aug-cc-pVDZ(-X2C) and 6–311+ +G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation…O and cation-π interactions, while Z− anions generally establish anion… H–O contacts. Predicted binding energies at the M06-2X/6–311+ +G(d,p) level range between−26.6 and−70.2 kcal/mol for cationic complexes and−20.4 and−62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O…cation…O interactions where the cation is trapped between O37 and O38 atoms of TXA0 . Anions do not behave uniformly towards TXA0 : while the fuoride anion F− induces the deprotonation of TXA0 , Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0 …Y+ and TXA0 …Z− complexes are mainly stabilized by electrostatic and inductive efects, whose combined contributions account for more than 60 percent of the total interaction energy.
- Full Text:
- Date Issued: 2023
Using Citizen Science to Protect Natural Untreated Drinking Water Sources: Natural Springs in Rural Catchments and B3 Municipalities in the Eastern Cape
- Mtati, Nosi, Chetty, Preven, Norman, Yondela, Mvulane, Paulose, Libala, Notiswa, Weaver, Matthew J T, Wolff, Margaret M, Cockburn, Jessica J, Mazibuko, Thembalani
- Authors: Mtati, Nosi , Chetty, Preven , Norman, Yondela , Mvulane, Paulose , Libala, Notiswa , Weaver, Matthew J T , Wolff, Margaret M , Cockburn, Jessica J , Mazibuko, Thembalani
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/425732 , vital:72279 , ISBN 978-0-6392-0550-2 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/3097 final.pdf
- Description: Citizen science is a well-known mechanism used by researchers to col-lect scientific data working together with citizens. It can also be used by interested and concerned citizens (social activists regarding environ-mental threats) to protect natural occurring things like biodiversity, rare species that are threatened extension and much more. It can be a natu-ral occurring process that evolves with time but it can also have some guidelines of how to monitor, collect, analyse and disseminate data. In this project we used participatory action research processes to co-develop tools (co-create being one of the types of citizen science) with local communities, using their knowledge of their area to monitor and protect natural springs. Springs are useful for providing drinking water for people but also for livestock. In rural areas and small towns where service delivery is not reliable, natural occurring water sources become the reliable supply for these communities. Springs also provide ecosys-tem services as they are a keystone ecological infrastructure. These natural water sources can be threatened by pollution, especially that of livestock which is mostly unattended, because they are sometimes shared by people and animals. This poses health risks to the users. This study co-developed the “spring protection and sustainable use” tool/s that can be used to guide communities and local government on how to protect these important water sources. Citizen science also cre-ates opportunities for learning to take place among the participants as well as the researchers involved.
- Full Text:
- Date Issued: 2023
- Authors: Mtati, Nosi , Chetty, Preven , Norman, Yondela , Mvulane, Paulose , Libala, Notiswa , Weaver, Matthew J T , Wolff, Margaret M , Cockburn, Jessica J , Mazibuko, Thembalani
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/425732 , vital:72279 , ISBN 978-0-6392-0550-2 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/3097 final.pdf
- Description: Citizen science is a well-known mechanism used by researchers to col-lect scientific data working together with citizens. It can also be used by interested and concerned citizens (social activists regarding environ-mental threats) to protect natural occurring things like biodiversity, rare species that are threatened extension and much more. It can be a natu-ral occurring process that evolves with time but it can also have some guidelines of how to monitor, collect, analyse and disseminate data. In this project we used participatory action research processes to co-develop tools (co-create being one of the types of citizen science) with local communities, using their knowledge of their area to monitor and protect natural springs. Springs are useful for providing drinking water for people but also for livestock. In rural areas and small towns where service delivery is not reliable, natural occurring water sources become the reliable supply for these communities. Springs also provide ecosys-tem services as they are a keystone ecological infrastructure. These natural water sources can be threatened by pollution, especially that of livestock which is mostly unattended, because they are sometimes shared by people and animals. This poses health risks to the users. This study co-developed the “spring protection and sustainable use” tool/s that can be used to guide communities and local government on how to protect these important water sources. Citizen science also cre-ates opportunities for learning to take place among the participants as well as the researchers involved.
- Full Text:
- Date Issued: 2023
Using Facebook user photos to quantify surface water dependency in Southern African arid-zone bird species
- Dixon, Elizabeth A, Smit, Ben
- Authors: Dixon, Elizabeth A , Smit, Ben
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441668 , vital:73905 , https://doi.org/10.1080/01584197.2023.2182223
- Description: Birds need to maintain their hydration by either gaining water from their food or by drinking surface water. Many arid-zone birds do not need to consume surface water to maintain body condition. Conservationists need to better understand avian use of surface water sources to inform management plans in a warming world. In this study, we explored the use of Facebook’s image search as a tool to predict interspecific variations in avian surface water use. There was a significant correlation between the proportion of Facebook photographs of each species associated with surface water, and surface water use indices for these species based on published field studies. These findings suggest that Facebook may be a useful source of data for determining the dependence of bird species on surface water. Future research could address the potential for Facebook and other social media platforms for answering a range of ecological questions relating to avian water dependency.
- Full Text:
- Date Issued: 2023
- Authors: Dixon, Elizabeth A , Smit, Ben
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441668 , vital:73905 , https://doi.org/10.1080/01584197.2023.2182223
- Description: Birds need to maintain their hydration by either gaining water from their food or by drinking surface water. Many arid-zone birds do not need to consume surface water to maintain body condition. Conservationists need to better understand avian use of surface water sources to inform management plans in a warming world. In this study, we explored the use of Facebook’s image search as a tool to predict interspecific variations in avian surface water use. There was a significant correlation between the proportion of Facebook photographs of each species associated with surface water, and surface water use indices for these species based on published field studies. These findings suggest that Facebook may be a useful source of data for determining the dependence of bird species on surface water. Future research could address the potential for Facebook and other social media platforms for answering a range of ecological questions relating to avian water dependency.
- Full Text:
- Date Issued: 2023
Vantage Points: Essays, Critical Perspectives, Field Notes, and a Manual.
- Muscatello, Mariagrazia, Touré, Ndèye Mané, Venturi, Francesco, Nicholson, Benjamin Ross, Krastin, Gavin, Rajeh, Omar, Hajimohammad, Saman, Tupajić, Tea
- Authors: Muscatello, Mariagrazia , Touré, Ndèye Mané , Venturi, Francesco , Nicholson, Benjamin Ross , Krastin, Gavin , Rajeh, Omar , Hajimohammad, Saman , Tupajić, Tea
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/469129 , vital:77212 , https://doi.org/10.3167/turba.2023.020205
- Description: A distinctive trait of the Chilean art scene, its insular condition came about as a consequence of the 1973 coup d’état, which interrupted foreign relations for a long time. The situation is only now being reversed, with local artistic production still being restricted to a homegrown market and audiences. Within this national circuit of the arts, almost entirely centered in the city of Santiago, artistic work is mostly limited to the activity of graduates and faculty from metropolitan universities, such as the Universidad de Chile and the Universidad Católica. The trend is now being reversed thanks to recent social events, primarily the 2019 uprisings or the increased market value of lithium, which put Chile back at the center of the global geopolitical agenda. In addition, a shift in media attention toward the art of indigenous peoples, which peaked in 2022, with examples such as the Venice Biennale, has allowed artists like Cecilia Vicuña, active since the seventies, to enter the so-called star system of art.
- Full Text:
- Date Issued: 2023
- Authors: Muscatello, Mariagrazia , Touré, Ndèye Mané , Venturi, Francesco , Nicholson, Benjamin Ross , Krastin, Gavin , Rajeh, Omar , Hajimohammad, Saman , Tupajić, Tea
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/469129 , vital:77212 , https://doi.org/10.3167/turba.2023.020205
- Description: A distinctive trait of the Chilean art scene, its insular condition came about as a consequence of the 1973 coup d’état, which interrupted foreign relations for a long time. The situation is only now being reversed, with local artistic production still being restricted to a homegrown market and audiences. Within this national circuit of the arts, almost entirely centered in the city of Santiago, artistic work is mostly limited to the activity of graduates and faculty from metropolitan universities, such as the Universidad de Chile and the Universidad Católica. The trend is now being reversed thanks to recent social events, primarily the 2019 uprisings or the increased market value of lithium, which put Chile back at the center of the global geopolitical agenda. In addition, a shift in media attention toward the art of indigenous peoples, which peaked in 2022, with examples such as the Venice Biennale, has allowed artists like Cecilia Vicuña, active since the seventies, to enter the so-called star system of art.
- Full Text:
- Date Issued: 2023
Water, Transport, Oil and Food: A Political–Economy–Ecology Lens on Changing Conceptions of Work, Learning and Skills Development in Africa
- Authors: Lotz-Sisitka, Heila
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/434894 , vital:73114 , ISBN 978-1529224634 , https://bristoluniversitypress.co.uk/transitioning-vocational-education-and-training-in-africa
- Description: Not enough has been said about the kinds of skills develop-ment that are needed if we are to stem the rising tides and impacts of political economies that have been driving what some call ‘fossil capital’(Malm, 2016). In this book, we are producing an emerging argument that it is necessary to also rethink and reframe vocational education and training (VET) logics and approaches if we are to fully consider the implica-tions of a warming future. This chapter provides the context of why this is such an urgent challenge and some thinking tools for understanding where we have come from and where we need to go. The prognosis is that it is now almost impossible to stop global warming below 2oC. The 2021 In-tergovernmental Panel on Climate Change (IPCC) report is-sued a ‘red alert’for humanity, noting climate change to be one of the most severe challenges facing human societies for decades and potentially centuries to come. Scientists are warning that we have entered a new ‘geological epoch’, named the ‘Anthropocene’, in which human activity, especial-ly the release of carbon dioxide into the atmosphere through fossil-based pollution, is transforming the stability of the earth system and creating knock on effects such as ice melt and methane release, which exacerbate the impacts of pollutants on the stability of the earth system.
- Full Text:
- Date Issued: 2023
- Authors: Lotz-Sisitka, Heila
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/434894 , vital:73114 , ISBN 978-1529224634 , https://bristoluniversitypress.co.uk/transitioning-vocational-education-and-training-in-africa
- Description: Not enough has been said about the kinds of skills develop-ment that are needed if we are to stem the rising tides and impacts of political economies that have been driving what some call ‘fossil capital’(Malm, 2016). In this book, we are producing an emerging argument that it is necessary to also rethink and reframe vocational education and training (VET) logics and approaches if we are to fully consider the implica-tions of a warming future. This chapter provides the context of why this is such an urgent challenge and some thinking tools for understanding where we have come from and where we need to go. The prognosis is that it is now almost impossible to stop global warming below 2oC. The 2021 In-tergovernmental Panel on Climate Change (IPCC) report is-sued a ‘red alert’for humanity, noting climate change to be one of the most severe challenges facing human societies for decades and potentially centuries to come. Scientists are warning that we have entered a new ‘geological epoch’, named the ‘Anthropocene’, in which human activity, especial-ly the release of carbon dioxide into the atmosphere through fossil-based pollution, is transforming the stability of the earth system and creating knock on effects such as ice melt and methane release, which exacerbate the impacts of pollutants on the stability of the earth system.
- Full Text:
- Date Issued: 2023
Wing-moult and seasonal occurrence of sunbirds (Nectariniidae) captured at four sites in the Eastern Cape, South Africa
- Bonnevie, Bo T, Craig, Adrian J F K, Hulley, Patrick E, Schultz, Albert, Tree, Anthony J
- Authors: Bonnevie, Bo T , Craig, Adrian J F K , Hulley, Patrick E , Schultz, Albert , Tree, Anthony J
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/449607 , vital:74833 , https://doi.org/10.2989/00306525.2022.2075482
- Description: Ringing activity in the Eastern Cape province, South Africa, spanned 30 years, with three sites active concurrently over a 14-year period, and three sites over a 6-year period. In total, in the course of 714 ringing days, in all months, we handled 1 207 Amethyst Sunbirds, 708 Southern Double-collared Sunbirds, 707 Greater Double-collared Sunbirds, 381 Grey Sunbirds, 121 Malachite Sunbirds and 140 Collared Sunbirds. Although individuals of all six species were recaptured more than five years after ringing, and despite evidence of the seasonal passage of sunbirds at two sites near the Indian Ocean coast, no birds were recaptured away from the original ringing site.
- Full Text:
- Date Issued: 2023
- Authors: Bonnevie, Bo T , Craig, Adrian J F K , Hulley, Patrick E , Schultz, Albert , Tree, Anthony J
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/449607 , vital:74833 , https://doi.org/10.2989/00306525.2022.2075482
- Description: Ringing activity in the Eastern Cape province, South Africa, spanned 30 years, with three sites active concurrently over a 14-year period, and three sites over a 6-year period. In total, in the course of 714 ringing days, in all months, we handled 1 207 Amethyst Sunbirds, 708 Southern Double-collared Sunbirds, 707 Greater Double-collared Sunbirds, 381 Grey Sunbirds, 121 Malachite Sunbirds and 140 Collared Sunbirds. Although individuals of all six species were recaptured more than five years after ringing, and despite evidence of the seasonal passage of sunbirds at two sites near the Indian Ocean coast, no birds were recaptured away from the original ringing site.
- Full Text:
- Date Issued: 2023
Women farmers leading and co-learning in an agroecology movement at the intersections of gender and climate
- Chanyau, Ludwig, Rosenberg, Eureta
- Authors: Chanyau, Ludwig , Rosenberg, Eureta
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/373873 , vital:66730 , xlink:href="https://doi.org/10.1080/10130950.2023.2239313"
- Description: This study, carried out in the Eastern Cape Province of South Africa, was particularly interested in women farmers’ access to social learning spaces for expanding their knowledge about farming in the context of climate change. Small-scale women and peasant farmers face historical intersectional inequalities as a result of the colonial and apartheid past which has continued to disadvantage women in the present through exclusion, limited or no access to finance, insecure or no land tenure, little bargaining power and unequal access to water. The gender prejudices and unequal access to resources experienced by women is brought into sharp relief by climate change. The article provides a case study of an agroecology movement led by women farmers that promotes climate-appropriate, low-cost farming practices using community and home gardens. The practices are tried out and further developed by women farmers themselves, relying on agroecology-informed extension services, open dialogue and the support of communities of practice. Unlike traditional top-down approaches to farmer learning common in public extension services, extension officers in the movement participate in creating conditions for co-learning and co-construction of new knowledge − that is, social learning − thus responding directly to their needs as farmers. The lead researcher joined in and observed farming and learning activities following an ethnographic approach. Farmers and other movement members were engaged in semi-structured interviews which explored the value derived from social learning (Wenger-Trayner and Wenger-Trayner Citation2020). The article concludes that the movement is responding to many of the intersectional challenges that women farmers in the Eastern Cape face. Further, its social learning approach holds potential for expanding women farmers’ ability to provide for themselves and their communities and inform their climate change adaptation.
- Full Text:
- Date Issued: 2023
- Authors: Chanyau, Ludwig , Rosenberg, Eureta
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/373873 , vital:66730 , xlink:href="https://doi.org/10.1080/10130950.2023.2239313"
- Description: This study, carried out in the Eastern Cape Province of South Africa, was particularly interested in women farmers’ access to social learning spaces for expanding their knowledge about farming in the context of climate change. Small-scale women and peasant farmers face historical intersectional inequalities as a result of the colonial and apartheid past which has continued to disadvantage women in the present through exclusion, limited or no access to finance, insecure or no land tenure, little bargaining power and unequal access to water. The gender prejudices and unequal access to resources experienced by women is brought into sharp relief by climate change. The article provides a case study of an agroecology movement led by women farmers that promotes climate-appropriate, low-cost farming practices using community and home gardens. The practices are tried out and further developed by women farmers themselves, relying on agroecology-informed extension services, open dialogue and the support of communities of practice. Unlike traditional top-down approaches to farmer learning common in public extension services, extension officers in the movement participate in creating conditions for co-learning and co-construction of new knowledge − that is, social learning − thus responding directly to their needs as farmers. The lead researcher joined in and observed farming and learning activities following an ethnographic approach. Farmers and other movement members were engaged in semi-structured interviews which explored the value derived from social learning (Wenger-Trayner and Wenger-Trayner Citation2020). The article concludes that the movement is responding to many of the intersectional challenges that women farmers in the Eastern Cape face. Further, its social learning approach holds potential for expanding women farmers’ ability to provide for themselves and their communities and inform their climate change adaptation.
- Full Text:
- Date Issued: 2023
‘Opera and music theatre’
- Authors: Brukman, Jeffrey J
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/468516 , vital:77086 , https://doi.org/10.1080/10137548.2023.2265252
- Description: In South Africa, from the first performances given by northern hemisphere-based touring companies in the 1800s through to the creation of state-funded Arts Councils used to promote high western culture during the time of apartheid, the opera genre has always occupied contested territory. Today, it still occupies disputed space with opera productions having to navigate difficult questions around cultural diversity, social relevance, societal inclusivity as well as financing. Despite the many successes of personal triumph and the creation of productions representing high standards of performance integrity, among the wider society opera is frequently considered to represent the cultural tastes of a small (often elite) minority. These concerns are common across the African continent from Cape Town to Cairo and beyond. In general, these issues are also replicated in terms of musical theatre.
- Full Text:
- Date Issued: 2023
- Authors: Brukman, Jeffrey J
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/468516 , vital:77086 , https://doi.org/10.1080/10137548.2023.2265252
- Description: In South Africa, from the first performances given by northern hemisphere-based touring companies in the 1800s through to the creation of state-funded Arts Councils used to promote high western culture during the time of apartheid, the opera genre has always occupied contested territory. Today, it still occupies disputed space with opera productions having to navigate difficult questions around cultural diversity, social relevance, societal inclusivity as well as financing. Despite the many successes of personal triumph and the creation of productions representing high standards of performance integrity, among the wider society opera is frequently considered to represent the cultural tastes of a small (often elite) minority. These concerns are common across the African continent from Cape Town to Cairo and beyond. In general, these issues are also replicated in terms of musical theatre.
- Full Text:
- Date Issued: 2023
“A Sort of Arcadian Country”: Plant-Life in Some Early South African Travelogues
- Authors: Wylie, Dan
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/458061 , vital:75713 , https://hdl.handle.net/10520/ejc-iseaeng_v50_n1_a1
- Description: Various branches of current ecocriticism are exploring ways of dismantling or at least diminishing dominant anthropocentric ways of evaluating the relationships among humans, the non-human world, and the literary imagination. Critical Animal Studies, Critical Plant Studies, and multispecies ecocriticism endeavour to re-evaluate the roles, even agency, of non-human life, as represented in literary works. This article unpacks the depiction of plants in three early South African travelogues (1795–1836), illuminating the sources of some enduring assumptions and iconic imageries in our relations with the natural world.
- Full Text:
- Date Issued: 2023
- Authors: Wylie, Dan
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/458061 , vital:75713 , https://hdl.handle.net/10520/ejc-iseaeng_v50_n1_a1
- Description: Various branches of current ecocriticism are exploring ways of dismantling or at least diminishing dominant anthropocentric ways of evaluating the relationships among humans, the non-human world, and the literary imagination. Critical Animal Studies, Critical Plant Studies, and multispecies ecocriticism endeavour to re-evaluate the roles, even agency, of non-human life, as represented in literary works. This article unpacks the depiction of plants in three early South African travelogues (1795–1836), illuminating the sources of some enduring assumptions and iconic imageries in our relations with the natural world.
- Full Text:
- Date Issued: 2023
A Change Project story: learning and caring for South Africa’s rivers
- Authors: Chetty, Preven
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/391060 , vital:68613 , xlink:href="https://eeasa.org.za/wp-content/uploads/2023/02/Final-EEASA-Bulletin-20212022-Final.pdf"
- Description: Water quality and scarcity is a major concern in Southern Africa and globally especially as the threat of climate change looms even closer. The current drought in South Africa and worsening rainfall has exposed the brittle nature of this country’s resilience to water shortages. Compounded to this is the fact that most rivers in South Africa are not adequately cared for and are under tremendous strain. Everyone who depends on these rivers whether directly or indirectly will soon be entering a new era where water will no longer be a ubiquitous commodity.
- Full Text:
- Date Issued: 2022
- Authors: Chetty, Preven
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/391060 , vital:68613 , xlink:href="https://eeasa.org.za/wp-content/uploads/2023/02/Final-EEASA-Bulletin-20212022-Final.pdf"
- Description: Water quality and scarcity is a major concern in Southern Africa and globally especially as the threat of climate change looms even closer. The current drought in South Africa and worsening rainfall has exposed the brittle nature of this country’s resilience to water shortages. Compounded to this is the fact that most rivers in South Africa are not adequately cared for and are under tremendous strain. Everyone who depends on these rivers whether directly or indirectly will soon be entering a new era where water will no longer be a ubiquitous commodity.
- Full Text:
- Date Issued: 2022
A Decolonial perspective on online media discourses in the context of violence against people with disabilities in South Africa
- Authors: Dalvit, Lorenzo
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/468140 , vital:77022 , DOI: 10.17231/comsoc.41(2022).3722
- Description: As one of the most violent and unequal societies globally, South Africa is still profoundly shaped by a legacy of segregation and oppression. While race, gender and socio-economic status receive much attention, (dis)ability is an important yet often neglected dimension of inequality. In this article, I adopt a decolonial perspective in discussing online media articles about violence against people with disabilities. By focusing on stories related to issues that received extensive media coverage (e.g. mental health, police brutality and gender-based violence), I problematise the Eurocentric human-rights discourse informing public and scholarly discussions. I also explore the link between current understandings of (dis)ability and the legacy of a violent colonial and apartheid past. As a result of the intersectional nature of (dis)ability, many of the stories involve multiple layers of inequality and different forms of oppression. An explicit focus on extreme forms of institutional and physical violence, while restricting the scope of enquiry, brings the brutality of western modernity and its effects on the people affected into sharp focus. Legal recurse appears to lead to incomplete reparation at best while its failures perpetuate a cycle of marginalisation and oppression. Rather than problematising these structural failures as a result of western modernity and neoliberalism, the media inadvertently obfuscates such links by performing its normative, that is, by identifying and exposing individual culprits or by blaming contextual factors.
- Full Text:
- Date Issued: 2022
- Authors: Dalvit, Lorenzo
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/468140 , vital:77022 , DOI: 10.17231/comsoc.41(2022).3722
- Description: As one of the most violent and unequal societies globally, South Africa is still profoundly shaped by a legacy of segregation and oppression. While race, gender and socio-economic status receive much attention, (dis)ability is an important yet often neglected dimension of inequality. In this article, I adopt a decolonial perspective in discussing online media articles about violence against people with disabilities. By focusing on stories related to issues that received extensive media coverage (e.g. mental health, police brutality and gender-based violence), I problematise the Eurocentric human-rights discourse informing public and scholarly discussions. I also explore the link between current understandings of (dis)ability and the legacy of a violent colonial and apartheid past. As a result of the intersectional nature of (dis)ability, many of the stories involve multiple layers of inequality and different forms of oppression. An explicit focus on extreme forms of institutional and physical violence, while restricting the scope of enquiry, brings the brutality of western modernity and its effects on the people affected into sharp focus. Legal recurse appears to lead to incomplete reparation at best while its failures perpetuate a cycle of marginalisation and oppression. Rather than problematising these structural failures as a result of western modernity and neoliberalism, the media inadvertently obfuscates such links by performing its normative, that is, by identifying and exposing individual culprits or by blaming contextual factors.
- Full Text:
- Date Issued: 2022
A laminated, emergentist view of skills ecosystems
- Ramsarup, Presha, Lotz-Sisitka, Heila, McGrath, Simon
- Authors: Ramsarup, Presha , Lotz-Sisitka, Heila , McGrath, Simon
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/370074 , vital:66295 , xlink:href="https://doi.org/10.1080/14767430.2022.2145768"
- Description: In this paper we present a model of vocational education and training (VET) that can be used to guide decisions relating to VET in Africa today. This model takes the critique of the neoclassical, neoliberal model of VET as its starting point. Guided by Bhaskar's Critical Naturalism, we use immanent critique to consider the adequacy of proposed alternatives to the neoclassical approach, such as: the heterodox approach, which foregrounds explanations based on human capital and political economy; and Hodgson and Spours' social ecosystem model, which addresses some of the limitations of the heterodox account by including, social and ecosystem elements. Finally, we offer a version of the social ecosystem model that, according to our analysis, explains more of the empirical evidence than previous models. Our version of the social ecosystem model differs from earlier versions in terms of its explicit reference to the critical realist ideas of position- practices and emergence.
- Full Text:
- Date Issued: 2022
- Authors: Ramsarup, Presha , Lotz-Sisitka, Heila , McGrath, Simon
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/370074 , vital:66295 , xlink:href="https://doi.org/10.1080/14767430.2022.2145768"
- Description: In this paper we present a model of vocational education and training (VET) that can be used to guide decisions relating to VET in Africa today. This model takes the critique of the neoclassical, neoliberal model of VET as its starting point. Guided by Bhaskar's Critical Naturalism, we use immanent critique to consider the adequacy of proposed alternatives to the neoclassical approach, such as: the heterodox approach, which foregrounds explanations based on human capital and political economy; and Hodgson and Spours' social ecosystem model, which addresses some of the limitations of the heterodox account by including, social and ecosystem elements. Finally, we offer a version of the social ecosystem model that, according to our analysis, explains more of the empirical evidence than previous models. Our version of the social ecosystem model differs from earlier versions in terms of its explicit reference to the critical realist ideas of position- practices and emergence.
- Full Text:
- Date Issued: 2022
A multiscale ONIOM study of the buckminsterfullerene (C60) Diels–Alder reaction: from model design to reaction path analysis
- Isamura, Bienfait K, Lobb, Kevin A
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452517 , vital:75140 , xlink:href=" https://link.springer.com/article/10.1007/s00894-022-05319-0"
- Description: The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels–Alder reaction of the buckminsterfullerene C60. Our computa-tions suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO3G) mod-el, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-of between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the efect of –OH and –CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces un-derpinning the process of cycloadduct formation.
- Full Text:
- Date Issued: 2022
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452517 , vital:75140 , xlink:href=" https://link.springer.com/article/10.1007/s00894-022-05319-0"
- Description: The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels–Alder reaction of the buckminsterfullerene C60. Our computa-tions suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO3G) mod-el, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-of between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the efect of –OH and –CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces un-derpinning the process of cycloadduct formation.
- Full Text:
- Date Issued: 2022
A simple quinoline-thiophene Schiff base turn-off chemosensor for Hg2+ detection
- Musikavanhu, Brian, Muthusamy, Selvaraj, Zhu, Dongwei, Xue, Zhaoli, Yu, Qian, Chivumba, Choonzo N, Mack, John, Nyokong, Tebello, Wang, Shengjun, Zhao, Long
- Authors: Musikavanhu, Brian , Muthusamy, Selvaraj , Zhu, Dongwei , Xue, Zhaoli , Yu, Qian , Chivumba, Choonzo N , Mack, John , Nyokong, Tebello , Wang, Shengjun , Zhao, Long
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/230362 , vital:49771 , xlink:href="https://doi.org/10.1016/j.saa.2021.120338"
- Description: A new Schiff base probe (QT) consisting of 8-aminoquinoline (Q) and thiophene-2-carboxaldehyde (T) moieties has been synthesized. QT undergoes chelation-enhanced fluorescence quenching when exposed to Hg2+ due to coordination by the sulfur and nitrogen atoms of QT thus forming a facile “turn-off” sensor. The formation of the chelation complex was confirmed by UV–visible absorption and emission spectral measurements, 1H NMR titration and density functional theory calculations. These studies revealed that the probe exhibits high selectivity and sensitivity towards Hg2+ in the presence of other common metal ions. A low detection limit of 23.4 nM was determined and a Job plot confirmed a 2:1 stoichiometry between QT and Hg2+. The potential utility of QT as a sensor for Hg2+ ions in human HeLa cells was determined by confocal fluorescence microscopy, and its suitability for use in the field with environmental samples was tested with Whatman filter paper strips.
- Full Text:
- Date Issued: 2022
- Authors: Musikavanhu, Brian , Muthusamy, Selvaraj , Zhu, Dongwei , Xue, Zhaoli , Yu, Qian , Chivumba, Choonzo N , Mack, John , Nyokong, Tebello , Wang, Shengjun , Zhao, Long
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/230362 , vital:49771 , xlink:href="https://doi.org/10.1016/j.saa.2021.120338"
- Description: A new Schiff base probe (QT) consisting of 8-aminoquinoline (Q) and thiophene-2-carboxaldehyde (T) moieties has been synthesized. QT undergoes chelation-enhanced fluorescence quenching when exposed to Hg2+ due to coordination by the sulfur and nitrogen atoms of QT thus forming a facile “turn-off” sensor. The formation of the chelation complex was confirmed by UV–visible absorption and emission spectral measurements, 1H NMR titration and density functional theory calculations. These studies revealed that the probe exhibits high selectivity and sensitivity towards Hg2+ in the presence of other common metal ions. A low detection limit of 23.4 nM was determined and a Job plot confirmed a 2:1 stoichiometry between QT and Hg2+. The potential utility of QT as a sensor for Hg2+ ions in human HeLa cells was determined by confocal fluorescence microscopy, and its suitability for use in the field with environmental samples was tested with Whatman filter paper strips.
- Full Text:
- Date Issued: 2022
A Sn (iv) porphyrin with mitochondria targeting properties for enhanced photodynamic activity against MCF-7 cells
- Babu, Balaji, Mack, John, Nyokong, Tebello
- Authors: Babu, Balaji , Mack, John , Nyokong, Tebello
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/230897 , vital:49829 , xlink:href="https://doi.org/10.1039/D2NJ00350C"
- Description: Two readily synthesized Sn(IV) porphyrins (SnP, SnPH) have been prepared with and without the cationic triphenylphosphonium moiety (TPP+), which have high singlet oxygen quantum yields (ca. 0.72) and long triplet state lifetimes. The Sn(IV) porphyrin with a TPP+ moiety (SnPH) exhibits favorable photodynamic activity against MCF-7 cells with IC50 values of 2.9 μM. SnPH exhibits higher cellular uptake than SnP in MCF-7 cells. A Rhodamine 123 (Rh123) assay showed that SnPH targets mitochondria and induces apoptosis by generating reactive oxygen species. The results demonstrate that this structural modification strategy merits further in-depth study.
- Full Text:
- Date Issued: 2022
- Authors: Babu, Balaji , Mack, John , Nyokong, Tebello
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/230897 , vital:49829 , xlink:href="https://doi.org/10.1039/D2NJ00350C"
- Description: Two readily synthesized Sn(IV) porphyrins (SnP, SnPH) have been prepared with and without the cationic triphenylphosphonium moiety (TPP+), which have high singlet oxygen quantum yields (ca. 0.72) and long triplet state lifetimes. The Sn(IV) porphyrin with a TPP+ moiety (SnPH) exhibits favorable photodynamic activity against MCF-7 cells with IC50 values of 2.9 μM. SnPH exhibits higher cellular uptake than SnP in MCF-7 cells. A Rhodamine 123 (Rh123) assay showed that SnPH targets mitochondria and induces apoptosis by generating reactive oxygen species. The results demonstrate that this structural modification strategy merits further in-depth study.
- Full Text:
- Date Issued: 2022
African birds as army ant followers
- Authors: Craig, Adrian J F K
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/448772 , vital:74759 , https://doi.org/10.1007/s10336-022-01987-0
- Description: Ant-following birds have been studied extensively in the Neotropics, but much less information is currently available for the Afrotropics. There are published records of 168 African bird species from 37 families foraging in association with driver ants (Dorylus, sub-family Dorylinae). However, of 52 bird species assessed as regular ant-followers, 38 belong to three families, which are disproportionately represented compared to other large Afrotropical bird families: Muscicapidae (18 spp.), Pycnonotidae (13 spp.) and Turdidae (7 spp.). The extent to which these birds are dependent on ants through their annual cycle is not known. African driver ants forage primarily under shaded, humid conditions by day, and may spend a month or longer underground. Conservation assessments of African forest habitats suggest that both driver ants and ant-following birds may be especially sensitive to the loss of forest cover.
- Full Text:
- Date Issued: 2022
- Authors: Craig, Adrian J F K
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/448772 , vital:74759 , https://doi.org/10.1007/s10336-022-01987-0
- Description: Ant-following birds have been studied extensively in the Neotropics, but much less information is currently available for the Afrotropics. There are published records of 168 African bird species from 37 families foraging in association with driver ants (Dorylus, sub-family Dorylinae). However, of 52 bird species assessed as regular ant-followers, 38 belong to three families, which are disproportionately represented compared to other large Afrotropical bird families: Muscicapidae (18 spp.), Pycnonotidae (13 spp.) and Turdidae (7 spp.). The extent to which these birds are dependent on ants through their annual cycle is not known. African driver ants forage primarily under shaded, humid conditions by day, and may spend a month or longer underground. Conservation assessments of African forest habitats suggest that both driver ants and ant-following birds may be especially sensitive to the loss of forest cover.
- Full Text:
- Date Issued: 2022
Age and growth of the Cape knifejaw Oplegnathus conwayi, an endemic South African teleost
- Foster, Ryan M, Childs, Amber-Robyn, Mann, Bruce Q, Potts, Warren M
- Authors: Foster, Ryan M , Childs, Amber-Robyn , Mann, Bruce Q , Potts, Warren M
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443128 , vital:74080 , https://doi.org/10.1080/15627020.2022.2035254
- Description: The South African spearfishery targets a variety of data-deficient species, which are consequently poorly managed. This study aimed to describe the age and growth of one of these species, the Cape knifejaw, Oplegnathus conwayi, which is endemic to the southern and eastern coasts of South Africa. Monthly biological samples were collected through research spearfishing (n = 170) and augmented by recreational spearfishers’ catches (n = 135). The results indicated that the O. conwayi population sex ratio was skewed towards males (1M:0.6F). The length- and age-frequency distributions were similar between sexes. Oplegnathus conwayi is a relatively slow-growing species, with a maximum-recorded age of 27 years. No significant differences were observed between male and female growth, with the overall population growth curve being best described as L(t) = 697.15(1 − e−0.06(t−6.30)). The slow growth observed in this species is characteristic of a species that is vulnerable to overexploitation, and accordingly a precautionary approach to future management is recommended.
- Full Text:
- Date Issued: 2022
- Authors: Foster, Ryan M , Childs, Amber-Robyn , Mann, Bruce Q , Potts, Warren M
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443128 , vital:74080 , https://doi.org/10.1080/15627020.2022.2035254
- Description: The South African spearfishery targets a variety of data-deficient species, which are consequently poorly managed. This study aimed to describe the age and growth of one of these species, the Cape knifejaw, Oplegnathus conwayi, which is endemic to the southern and eastern coasts of South Africa. Monthly biological samples were collected through research spearfishing (n = 170) and augmented by recreational spearfishers’ catches (n = 135). The results indicated that the O. conwayi population sex ratio was skewed towards males (1M:0.6F). The length- and age-frequency distributions were similar between sexes. Oplegnathus conwayi is a relatively slow-growing species, with a maximum-recorded age of 27 years. No significant differences were observed between male and female growth, with the overall population growth curve being best described as L(t) = 697.15(1 − e−0.06(t−6.30)). The slow growth observed in this species is characteristic of a species that is vulnerable to overexploitation, and accordingly a precautionary approach to future management is recommended.
- Full Text:
- Date Issued: 2022
Agents of Change: Journalism Education as Critical Service-Learning
- Authors: Du Toit, Jeanne E
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/468250 , vital:77036 , ISBN 978-1-80071-188-4 , https://www.emerald.com/insight/content/doi/10.1108/s2055-364120220000046004/full/html
- Description: The chapter deals with a service-learning course based in the School of Journalism and Media Studies at Rhodes University in South Africa. It provides a backdrop for the case study, describing the context in which the course is based and kind of intervention that it aims to make into this context. It then maps out the theoretical framework that informs the course, explaining how this is informed by the available spectrum of approaches to service-learning. It demonstrates how the course draws on the concept of a ‘communicative ecology’, to provide itself with a language in which to reflect on the social significance of communication. The chapter then reviews the first cycle of the course which took place in 2019, drawing on insights from participants (teachers, students and community partners). It deals, firstly, with the participants’ engagement with the concept of service-learning. Secondly, it describes their experience of service-learning as a communicative process. Finally, it describes their evaluation of this process as an intervention into the local communicative ecology. It is demonstrated that service-learning enables the school to respond strategically to the need for innovative communicative practices both in their immediate environment and within the broader South African context.
- Full Text:
- Date Issued: 2022
- Authors: Du Toit, Jeanne E
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/468250 , vital:77036 , ISBN 978-1-80071-188-4 , https://www.emerald.com/insight/content/doi/10.1108/s2055-364120220000046004/full/html
- Description: The chapter deals with a service-learning course based in the School of Journalism and Media Studies at Rhodes University in South Africa. It provides a backdrop for the case study, describing the context in which the course is based and kind of intervention that it aims to make into this context. It then maps out the theoretical framework that informs the course, explaining how this is informed by the available spectrum of approaches to service-learning. It demonstrates how the course draws on the concept of a ‘communicative ecology’, to provide itself with a language in which to reflect on the social significance of communication. The chapter then reviews the first cycle of the course which took place in 2019, drawing on insights from participants (teachers, students and community partners). It deals, firstly, with the participants’ engagement with the concept of service-learning. Secondly, it describes their experience of service-learning as a communicative process. Finally, it describes their evaluation of this process as an intervention into the local communicative ecology. It is demonstrated that service-learning enables the school to respond strategically to the need for innovative communicative practices both in their immediate environment and within the broader South African context.
- Full Text:
- Date Issued: 2022
Alignment, scaling and resourcing of citizen-based water quality monitoring Initiatives
- Lotz-Sisitka, Heila, Ward, Mike, Taylor, Jim, Vallabh, Priya, Madiba, Morakane, Graham, P Mark, Louw, Adrienne J, Brownell, Faye
- Authors: Lotz-Sisitka, Heila , Ward, Mike , Taylor, Jim , Vallabh, Priya , Madiba, Morakane , Graham, P Mark , Louw, Adrienne J , Brownell, Faye
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/435729 , vital:73195 , ISBN 978-0-6392-0344-7 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2854%20final.pdf
- Description: This action-oriented research project seeks to address the policy-practice contradiction that exists between commit-ments and requirements for citizen engagement and in-volvement in Integrated Water Quality Management (IWQM) and a lack of sustainable support for scaling high quality Citi-zen-based Water Quality Monitoring (CBWQM) practices that exist in South Africa.
- Full Text:
- Date Issued: 2022
- Authors: Lotz-Sisitka, Heila , Ward, Mike , Taylor, Jim , Vallabh, Priya , Madiba, Morakane , Graham, P Mark , Louw, Adrienne J , Brownell, Faye
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/435729 , vital:73195 , ISBN 978-0-6392-0344-7 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2854%20final.pdf
- Description: This action-oriented research project seeks to address the policy-practice contradiction that exists between commit-ments and requirements for citizen engagement and in-volvement in Integrated Water Quality Management (IWQM) and a lack of sustainable support for scaling high quality Citi-zen-based Water Quality Monitoring (CBWQM) practices that exist in South Africa.
- Full Text:
- Date Issued: 2022
AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis
- Isamura, Bienfait K, Lobb, Kevin A
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453143 , vital:75226 , xlink:href="https://link.springer.com/article/10.1186/s13321-022-00618-3"
- Description: Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication reports technical details and preliminary results of a python-based tool (AMADAR) designed to generate any Diels–Alder (DA) transition state geometry (TS) and analyze determined IRC paths in a (quasi-)automated fashion, given the product SMILES. Two modules of the package are devoted to performing, from IRC paths, reaction force analyses (RFA) and atomic (fragment) decompositions of the reaction force F and reaction force constant κ. The performance of the protocol has been assessed using a dataset of 2000 DA cycloadducts retrieved from the ZINC database. The sequential location of the corresponding TSs was achieved with a success rate of 95%. RFA plots confrmed the reaction force constant κ to be a good indicator of the (non)synchronicity of the associated DA reactions. Moreover, the atomic decomposition of κ allows for the rationalization of the (a)synchronicity of each DA reaction in terms of contributions stemming from pairs of interacting atoms. The source code of the AMADAR tool is available on GitHub [CMCDD/AMADAR(github. com)] and can be used directly with minor customizations, mostly regarding the local working environment of the user.
- Full Text:
- Date Issued: 2022
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453143 , vital:75226 , xlink:href="https://link.springer.com/article/10.1186/s13321-022-00618-3"
- Description: Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication reports technical details and preliminary results of a python-based tool (AMADAR) designed to generate any Diels–Alder (DA) transition state geometry (TS) and analyze determined IRC paths in a (quasi-)automated fashion, given the product SMILES. Two modules of the package are devoted to performing, from IRC paths, reaction force analyses (RFA) and atomic (fragment) decompositions of the reaction force F and reaction force constant κ. The performance of the protocol has been assessed using a dataset of 2000 DA cycloadducts retrieved from the ZINC database. The sequential location of the corresponding TSs was achieved with a success rate of 95%. RFA plots confrmed the reaction force constant κ to be a good indicator of the (non)synchronicity of the associated DA reactions. Moreover, the atomic decomposition of κ allows for the rationalization of the (a)synchronicity of each DA reaction in terms of contributions stemming from pairs of interacting atoms. The source code of the AMADAR tool is available on GitHub [CMCDD/AMADAR(github. com)] and can be used directly with minor customizations, mostly regarding the local working environment of the user.
- Full Text:
- Date Issued: 2022