PAMD - Practical Applications of Molecular Dynamic Simulations

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PAMD - Practical Applications of Molecular Dynamic Simulations (en)
Authors

Publications

Ispitivanje međumolekulskih interakcija računarskim simulacijama

Zarić, Milana; Kijevčanin, Mirjana; Radović, Ivona

(Belgrade : Serbian Chemical Society, 2023)

TY  - CONF
AU  - Zarić, Milana
AU  - Kijevčanin, Mirjana
AU  - Radović, Ivona
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7244
AB  - Експериментална мерења и подаци су од суштинског значаја за пружање 
информација о својствима и понашању смеша. Међутим, компјутерски прорачуни у комбинацији са експерименталним мерењем могу пружити дубљи увид у понашање и интеракције на молекулском нивоу. За течне бинарне смеше нековалентне интеракције су проучаване квантним хемијским прорачунима и молекулско-динамичким симулацијама. Истражен је утицај различитих функционалних група,  попут двоструке везе са могућношћу π-π интеракције и -ОН групе са могућношћу водоничне везе. Поред тога, проучавали смо утицај геометрије молекула на својства бинарних смеша.
AB  - Experimental measurement and data are essential for providing the information of properties and behavior of mixtures. However, the computer calculations combined with experimental measurement can provide a deeper insight of behavior and interactions at the molecular level. For liquid binary mixtures the non-covalent interactions were studied with quantum chemical calculations and molecular dynamic simulations. The influence of different functional groups, like the double bond with possibility for the π-π interactions and the -OH group with possibility for the hydrogen bonding was investigated. In addition, we studied the influence of the geometry of the molecule on the properties of binary mixture.
PB  - Belgrade : Serbian Chemical Society
C3  - Kratki izvodi radova, knjiga radova - 59. Savetovanje Srpskog hemijskog društva, 1. i 2. jun 2023. godine, Novi Sad / Book of Abstracts, Proceedings - 59th Meeting of the Serbian Chemical Society, June 1-2, 2023, Novi Sad, Serbia
T1  - Ispitivanje međumolekulskih interakcija računarskim  simulacijama
T1  - Investigation of intermolecular interactions using computer  simulations
SP  - 137
EP  - 137
UR  - https://hdl.handle.net/21.15107/rcub_cer_7244
ER  - 
@conference{
author = "Zarić, Milana and Kijevčanin, Mirjana and Radović, Ivona",
year = "2023",
abstract = "Експериментална мерења и подаци су од суштинског значаја за пружање 
информација о својствима и понашању смеша. Међутим, компјутерски прорачуни у комбинацији са експерименталним мерењем могу пружити дубљи увид у понашање и интеракције на молекулском нивоу. За течне бинарне смеше нековалентне интеракције су проучаване квантним хемијским прорачунима и молекулско-динамичким симулацијама. Истражен је утицај различитих функционалних група,  попут двоструке везе са могућношћу π-π интеракције и -ОН групе са могућношћу водоничне везе. Поред тога, проучавали смо утицај геометрије молекула на својства бинарних смеша., Experimental measurement and data are essential for providing the information of properties and behavior of mixtures. However, the computer calculations combined with experimental measurement can provide a deeper insight of behavior and interactions at the molecular level. For liquid binary mixtures the non-covalent interactions were studied with quantum chemical calculations and molecular dynamic simulations. The influence of different functional groups, like the double bond with possibility for the π-π interactions and the -OH group with possibility for the hydrogen bonding was investigated. In addition, we studied the influence of the geometry of the molecule on the properties of binary mixture.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Kratki izvodi radova, knjiga radova - 59. Savetovanje Srpskog hemijskog društva, 1. i 2. jun 2023. godine, Novi Sad / Book of Abstracts, Proceedings - 59th Meeting of the Serbian Chemical Society, June 1-2, 2023, Novi Sad, Serbia",
title = "Ispitivanje međumolekulskih interakcija računarskim  simulacijama, Investigation of intermolecular interactions using computer  simulations",
pages = "137-137",
url = "https://hdl.handle.net/21.15107/rcub_cer_7244"
}
Zarić, M., Kijevčanin, M.,& Radović, I.. (2023). Ispitivanje međumolekulskih interakcija računarskim  simulacijama. in Kratki izvodi radova, knjiga radova - 59. Savetovanje Srpskog hemijskog društva, 1. i 2. jun 2023. godine, Novi Sad / Book of Abstracts, Proceedings - 59th Meeting of the Serbian Chemical Society, June 1-2, 2023, Novi Sad, Serbia
Belgrade : Serbian Chemical Society., 137-137.
https://hdl.handle.net/21.15107/rcub_cer_7244
Zarić M, Kijevčanin M, Radović I. Ispitivanje međumolekulskih interakcija računarskim  simulacijama. in Kratki izvodi radova, knjiga radova - 59. Savetovanje Srpskog hemijskog društva, 1. i 2. jun 2023. godine, Novi Sad / Book of Abstracts, Proceedings - 59th Meeting of the Serbian Chemical Society, June 1-2, 2023, Novi Sad, Serbia. 2023;:137-137.
https://hdl.handle.net/21.15107/rcub_cer_7244 .
Zarić, Milana, Kijevčanin, Mirjana, Radović, Ivona, "Ispitivanje međumolekulskih interakcija računarskim  simulacijama" in Kratki izvodi radova, knjiga radova - 59. Savetovanje Srpskog hemijskog društva, 1. i 2. jun 2023. godine, Novi Sad / Book of Abstracts, Proceedings - 59th Meeting of the Serbian Chemical Society, June 1-2, 2023, Novi Sad, Serbia (2023):137-137,
https://hdl.handle.net/21.15107/rcub_cer_7244 .

Thermodynamic properties of binary mixtures: experimental and computational methodology

Zarić, Milana; Radović, Ivona; Kijevčanin, Mirjana

(University of East Sarajevo, Faculty of Technology, 2023)

TY  - CONF
AU  - Zarić, Milana
AU  - Radović, Ivona
AU  - Kijevčanin, Mirjana
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7245
AB  - Insight in different types of mixtures’ properties has a great impact in understanding and 
predicting the behavior of mixtures. The properties of liquid mixtures, such as volumetric and 
transport properties depend on the geometry and steric effects, however, they also depend on 
noncovalent interactions between molecules. The behavior depends on the functional groups of 
molecules; the functional groups that were investigated in our work were double bond and -OH 
group. Double bonds are present in many structures, like fatty acids and have role in many 
processes, like in polymerization and petrochemical processes. In order to investigate the 
influence of double bond and -OH group, two sets of mixtures are investigated: (1) n-hexane + 
1-hexanol and n-hexane + cis-3-hexen-1-ol and (2) n-octane + 1-hexanol and 1-octene + 1-
hexanol. The mixtures are examined experimentally and theoretically. Experimental aspect 
includes measurement of thermodynamic and transport properties: density and viscosity at the 
whole composition range at various temperatures, from (288.15 to 318.15) K. Based on the 
experimental data, excess molar volumes (VE
) and viscosity deviations (Δη) were calculated and 
for fitting the calculated data the Redlich-Kister equation was used. The theoretical aspect 
includes two methods: quantum mechanical calculations and simulations with Molecular 
Dynamic (MD). Quantum mechanical calculations provide information of the intermolecular 
interactions between two molecules. It also provides information about the geometry and 
interaction energies between molecules. It is done on model systems representing the influence 
of the functional groups; double bond and -OH group. Molecular Dynamics is a good tool for 
connecting the microscopic and macroscopic properties. The MD is based on the solving step by-step the equation of motion, predicting the dynamics of the system. MD simulations were 
performed in GROMACS using the simulation time of 2 ns. The combination of experimental and 
theoretical studies gives a good knowledge on the properties of the mixtures, as well as 
explanation and understanding of these properties.
PB  - University of East Sarajevo, Faculty of Technology
C3  - Book of abstracts - VIII International Congress “Engineering, Environment and Materials in Process Industry“ (EEM2023), March 20-23, Jahorina, Republic of Srpska, Bosnia and Herzegvina
T1  - Thermodynamic properties of binary mixtures: experimental and computational methodology
SP  - 171
EP  - 171
UR  - https://hdl.handle.net/21.15107/rcub_cer_7245
ER  - 
@conference{
author = "Zarić, Milana and Radović, Ivona and Kijevčanin, Mirjana",
year = "2023",
abstract = "Insight in different types of mixtures’ properties has a great impact in understanding and 
predicting the behavior of mixtures. The properties of liquid mixtures, such as volumetric and 
transport properties depend on the geometry and steric effects, however, they also depend on 
noncovalent interactions between molecules. The behavior depends on the functional groups of 
molecules; the functional groups that were investigated in our work were double bond and -OH 
group. Double bonds are present in many structures, like fatty acids and have role in many 
processes, like in polymerization and petrochemical processes. In order to investigate the 
influence of double bond and -OH group, two sets of mixtures are investigated: (1) n-hexane + 
1-hexanol and n-hexane + cis-3-hexen-1-ol and (2) n-octane + 1-hexanol and 1-octene + 1-
hexanol. The mixtures are examined experimentally and theoretically. Experimental aspect 
includes measurement of thermodynamic and transport properties: density and viscosity at the 
whole composition range at various temperatures, from (288.15 to 318.15) K. Based on the 
experimental data, excess molar volumes (VE
) and viscosity deviations (Δη) were calculated and 
for fitting the calculated data the Redlich-Kister equation was used. The theoretical aspect 
includes two methods: quantum mechanical calculations and simulations with Molecular 
Dynamic (MD). Quantum mechanical calculations provide information of the intermolecular 
interactions between two molecules. It also provides information about the geometry and 
interaction energies between molecules. It is done on model systems representing the influence 
of the functional groups; double bond and -OH group. Molecular Dynamics is a good tool for 
connecting the microscopic and macroscopic properties. The MD is based on the solving step by-step the equation of motion, predicting the dynamics of the system. MD simulations were 
performed in GROMACS using the simulation time of 2 ns. The combination of experimental and 
theoretical studies gives a good knowledge on the properties of the mixtures, as well as 
explanation and understanding of these properties.",
publisher = "University of East Sarajevo, Faculty of Technology",
journal = "Book of abstracts - VIII International Congress “Engineering, Environment and Materials in Process Industry“ (EEM2023), March 20-23, Jahorina, Republic of Srpska, Bosnia and Herzegvina",
title = "Thermodynamic properties of binary mixtures: experimental and computational methodology",
pages = "171-171",
url = "https://hdl.handle.net/21.15107/rcub_cer_7245"
}
Zarić, M., Radović, I.,& Kijevčanin, M.. (2023). Thermodynamic properties of binary mixtures: experimental and computational methodology. in Book of abstracts - VIII International Congress “Engineering, Environment and Materials in Process Industry“ (EEM2023), March 20-23, Jahorina, Republic of Srpska, Bosnia and Herzegvina
University of East Sarajevo, Faculty of Technology., 171-171.
https://hdl.handle.net/21.15107/rcub_cer_7245
Zarić M, Radović I, Kijevčanin M. Thermodynamic properties of binary mixtures: experimental and computational methodology. in Book of abstracts - VIII International Congress “Engineering, Environment and Materials in Process Industry“ (EEM2023), March 20-23, Jahorina, Republic of Srpska, Bosnia and Herzegvina. 2023;:171-171.
https://hdl.handle.net/21.15107/rcub_cer_7245 .
Zarić, Milana, Radović, Ivona, Kijevčanin, Mirjana, "Thermodynamic properties of binary mixtures: experimental and computational methodology" in Book of abstracts - VIII International Congress “Engineering, Environment and Materials in Process Industry“ (EEM2023), March 20-23, Jahorina, Republic of Srpska, Bosnia and Herzegvina (2023):171-171,
https://hdl.handle.net/21.15107/rcub_cer_7245 .

Termodinamička svojstva i modelovanje međumolekulske interakcije dvokomponentne smeše limonena i hloroforma

Grozdanić, Nikola; Zarić, Milana; Krupez, Bojana; Kijevčanin, Mirjana; Radović, Ivona

(Belgrade : Serbian Chemical Society, 2021)

TY  - CONF
AU  - Grozdanić, Nikola
AU  - Zarić, Milana
AU  - Krupez, Bojana
AU  - Kijevčanin, Mirjana
AU  - Radović, Ivona
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7246
AB  - U cilju proučavanja termodinamičkih svojstava binarne smeše limonen + hloroform eksperimentalno su određene gustine (ρ), viskoznosti (η) i indeksi refrakcije (nD) za ovu smešu. Eksperimentalna merenja su rađena u opsegu temperatura od 288,15 do 323,15 K na atmosferskom pritisku, za ceo opseg udela. Na osnovu eksperimentalno dobijenih rezultata izračunate su vrednosti 
dopunske molarne zapremine VE, vrednosti promene viskoznosti ∆η i vrednosti promene indeksa refrakcije ∆nD. Za izvedene vrednosti rezultati su dobijeni fitovanjem Redlich-Kister polinomskom jednačinom. Na osnovu ovih rezultata izvedeni su zaključci o međumolekulskim interakcijama u limonen + hloroform binarnom sistemu. Vrednosti dopunske molarne zapremine, kao i vrednosti promene viskoznosti i indeksa refrakcije pokazuju pozitivno odstupanje u celom opsegu molskih udela. Povećanje dopunske molarne zapremine pokazuje da je pakovanje molekula u smeši manje efikasno nego u čistim komponentama.
AB  - In order to study the thermodynamic properties of the binary mixture limonene + chloroform, the densities (ρ), viscosities (η) and refractive indices (nD) for this mixture were experimentally determined. Experimental measurements were performed in the temperature range from 288.15 K to 323.15 K at atmospheric pressure, for the entire range of composition. Based on the experimental results, the values of excess molar volume VE, the viscosity deviation ∆η and the refractive index deviation ∆nD were calculated. Additionally, the excess molar volume and viscosity and refractive indecies deviations were fitted with the Redlich-Kister polynomial equation. Based on these results, conclusions can be made on intermolecular interactions in the limonene + chloroform 
binary system. Values of excess molar volume, viscosity and refractive index deviations have shown a postive non-ideal behavior in the entire composition range. An increase in the values of exces molar volume indicates that the packaging of the molecules in the mixture is less efficient than in the pure components.
PB  - Belgrade : Serbian Chemical Society
C3  - Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia
T1  - Termodinamička svojstva i modelovanje međumolekulske interakcije  dvokomponentne smeše limonena i hloroforma
T1  - Thermodynamic properties and modeling intermolecular interaction of binary  mixture of limonene and chloroform
SP  - 115
EP  - 120
UR  - https://hdl.handle.net/21.15107/rcub_cer_7246
ER  - 
@conference{
author = "Grozdanić, Nikola and Zarić, Milana and Krupez, Bojana and Kijevčanin, Mirjana and Radović, Ivona",
year = "2021",
abstract = "U cilju proučavanja termodinamičkih svojstava binarne smeše limonen + hloroform eksperimentalno su određene gustine (ρ), viskoznosti (η) i indeksi refrakcije (nD) za ovu smešu. Eksperimentalna merenja su rađena u opsegu temperatura od 288,15 do 323,15 K na atmosferskom pritisku, za ceo opseg udela. Na osnovu eksperimentalno dobijenih rezultata izračunate su vrednosti 
dopunske molarne zapremine VE, vrednosti promene viskoznosti ∆η i vrednosti promene indeksa refrakcije ∆nD. Za izvedene vrednosti rezultati su dobijeni fitovanjem Redlich-Kister polinomskom jednačinom. Na osnovu ovih rezultata izvedeni su zaključci o međumolekulskim interakcijama u limonen + hloroform binarnom sistemu. Vrednosti dopunske molarne zapremine, kao i vrednosti promene viskoznosti i indeksa refrakcije pokazuju pozitivno odstupanje u celom opsegu molskih udela. Povećanje dopunske molarne zapremine pokazuje da je pakovanje molekula u smeši manje efikasno nego u čistim komponentama., In order to study the thermodynamic properties of the binary mixture limonene + chloroform, the densities (ρ), viscosities (η) and refractive indices (nD) for this mixture were experimentally determined. Experimental measurements were performed in the temperature range from 288.15 K to 323.15 K at atmospheric pressure, for the entire range of composition. Based on the experimental results, the values of excess molar volume VE, the viscosity deviation ∆η and the refractive index deviation ∆nD were calculated. Additionally, the excess molar volume and viscosity and refractive indecies deviations were fitted with the Redlich-Kister polynomial equation. Based on these results, conclusions can be made on intermolecular interactions in the limonene + chloroform 
binary system. Values of excess molar volume, viscosity and refractive index deviations have shown a postive non-ideal behavior in the entire composition range. An increase in the values of exces molar volume indicates that the packaging of the molecules in the mixture is less efficient than in the pure components.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia",
title = "Termodinamička svojstva i modelovanje međumolekulske interakcije  dvokomponentne smeše limonena i hloroforma, Thermodynamic properties and modeling intermolecular interaction of binary  mixture of limonene and chloroform",
pages = "115-120",
url = "https://hdl.handle.net/21.15107/rcub_cer_7246"
}
Grozdanić, N., Zarić, M., Krupez, B., Kijevčanin, M.,& Radović, I.. (2021). Termodinamička svojstva i modelovanje međumolekulske interakcije  dvokomponentne smeše limonena i hloroforma. in Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia
Belgrade : Serbian Chemical Society., 115-120.
https://hdl.handle.net/21.15107/rcub_cer_7246
Grozdanić N, Zarić M, Krupez B, Kijevčanin M, Radović I. Termodinamička svojstva i modelovanje međumolekulske interakcije  dvokomponentne smeše limonena i hloroforma. in Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia. 2021;:115-120.
https://hdl.handle.net/21.15107/rcub_cer_7246 .
Grozdanić, Nikola, Zarić, Milana, Krupez, Bojana, Kijevčanin, Mirjana, Radović, Ivona, "Termodinamička svojstva i modelovanje međumolekulske interakcije  dvokomponentne smeše limonena i hloroforma" in Kratki izvodi radova, Knjiga radova 57. Savetovanje Srpskog hemijskog društva, 18. i 19. juni 2021, Kragujevac / Book of abstracts, Proceedings - 57th Meeting of the Serbian Chemical Society, June 18-19, 2021, Kragujevac, Serbia (2021):115-120,
https://hdl.handle.net/21.15107/rcub_cer_7246 .