Supplementary Information revista.iq.unesp.br | Vol. 47 | special issue 1 | 2022 | 57 Eclética Química Journal, vol. 47, special issue 1, 2022, 57-62 ISSN: 1678-4618 DOI: 10.26850/1678-4618eqj.v47.1SI.2022.p57-62 Comparative study of benznidazole encapsulation in boron nitride and carbon nanotubes: A quantum chemistry study Jeziel Rodrigues dos Santos1+ , Osmair Vital de Oliveira2 , Rafael Giordano Viegas2 , José Divino dos Santos3 , Elson Longo1 1. Federal University of Sao Carlos, Center for the Development of Functional Materials, São Carlos, Brazil. 2. Federal Institute of Education Science and Technology of São Paulo, Catanduva, Brazil. 3. Goiás State University, Department of Chemistry, Anápolis, Brazil. +Corresponding author: Jeziel Rodrigues dos Santos, Phone: +5562981791374, Email address: prof.jeziel@gmail.com ARTICLE INFO Article history: Received: July 19, 2021 Accepted: October 19, 2021 Published: April 11, 2022 Keywords: 1. BNNT 2. CNT 3. benznidazole 4. encapsulation 5. chagas disease 6. DFT Section Editors: Elson Longo and Juan Manuel Andrés Bort S1. Script to generate cartesian coordinates for BNNT and CNT models. #!/bin/bash #UEG - UnUCET - Nanotubos das formas [(XY)n]m, com n e m PARES E IMPARES #FORMA ZIG-ZAG ou BARCO - v.08 #Dr. José Divino dos Santos e MsC.Jeziel Rodrigues #como execultar: ./shell-nano-otim-xy-par-impar.sh $1 $2 $3 $4 $5 $6 $7 $8 $9 $10 $11 $12 $13 $14 pi=` echo "scale=10;4*a(1)"|bc -l ` n0=$1 #Numero de atomos na base GaAs, ZnO, C, BN ... m=$2 #Numero de niveis do nanotubo d=$3 #distancia X-X tipo=$4 #tipo de crescimento - zig ou bar atomo1=$5 #Simbolo atomico 1 atomo2=$6 #Simbolo atomico 2 metodo=$7 #Metodo semiempirico - MNDO, AM1, PM3 multi=$8 #Multiplicidades - SINGLET, DOUBLET, TRIPLET, QUARTET ... carga=$9 #Cargas - +2, +1, 0, -1, -2 ... shift;shift;shift;shift;shift;shift;shift;shift;shift; metodoAb=$1 #Metodo Ab-initio: HF, RHF, UHF, DFT, ... baseAb=$2 #Base Ab-initio: 3-21G, 6-31G, lanl2dz, GEN, ... multiAb=$3 #Multiplicidades abinitio: 1, 2, 3, 4 ... cargaAb=$4 #Cargas - +2, +1, 0, -1, -2 ... grad=$5 #Gradiente procurado fatd1=1.0 #fator de D1=fatd1*D1 fatd2=1.0 #fator de D2=fatd2*D2 fatd3=1.0 #fator de D3=fatd3*D3 https://revista.iq.unesp.br/index.php/ecletica https://revista.iq.unesp.br/index.php/ecletica https://doi.org/10.26850/1678-4618eqj.v47.1SI.2022.p57-62 mailto:prof.jeziel@gmail.com http://orcid.org/0000-0002-3147-4757 http://orcid.org/0000-0001-9463-2567 http://orcid.org/0000-0002-6102-3375 http://orcid.org/0000-0002-9272-414X http://orcid.org/0000-0001-8062-7791 Supplementary Information revista.iq.unesp.br 58 Eclética Química Journal, vol. 47, special issue 1, 2022, 57-62 ISSN: 1678-4618 DOI: 10.26850/1678-4618eqj.v47.1SI.2022.p57-62 otimd=1.0 #otimizador de distancia otima=1.0 #otimizador de angulo otimt=1.0 #otimizador de torsao #Exemplos: if [ "${tipo}" = "zig" ] then #Crescimento ZIG-ZAG n=` echo "${n0}"|bc -l ` #numero de atomos X na base nome=nano${tipo}-${atomo1}${atomo2}-n${n}-m${m}-${metodo}-${multi}- c${carga} te=` echo "scale=10;(0.0000*2*${pi}/${n})"|bc -l ` #angulo inicial; zero grau dte=` echo "scale=10;(2*${pi}/${n})"|bc -l ` #incremento do angulo D1=`echo "scale=10;${fatd1}*(2*${d}*c(${pi}/6))"|bc -l ` # distancia basica X-X ra=`echo "scale=10;(${D1})/(sqrt(2 - 2*c(2*${pi}/${n})))"|bc -l ` #raio ZIG-ZAG #curv=`echo "scale=10;1/${ra}"|bc -l ` # distancia basica do ZIG-ZAG inc1=0.00000 inc2=` echo "scale=10;1.0000*(${pi}/${n})"|bc -l ` #angulo inicial de Y incte=` echo "scale=10;1.0000*(${pi}/${n})"|bc -l ` #incremento do angulo no nivel D2=`echo "scale=10;${fatd2}*(${d}*s(${pi}/6))"|bc -l ` # incr D2*fat2 D3=`echo "scale=10;${fatd3}*(${d} + ${d}*s(${pi}/6))"|bc -l ` # incr D3*fat3 tx=`echo "scale=10;-${ra}*c(${te} + ${inc1})"|bc -l ` #translacao em x ty=`echo "scale=10;-${ra}*s(${te} + ${inc1})"|bc -l ` #translacao em y z2=`echo "scale=10;0.0000*s(${pi}/6)"|bc -l ` #coord z2 # echo " ${metodo} PREC SHIFT1000 DEBUG LET T=1999999 + " > ${nome}.dat # echo " DUMP=250000 XYZ PL GEO-OK ${multi} CHARGE=${carga} " >> ${nome}.dat echo " ${metodo} UHF CYCLES=30000 PREC SHIFT1000 DEBUG LET T=19999999 + " > ${nome}.dat echo " DUMP=250000 AUX GNORM=0.01 PL GEO-OK ${multi} CHARGE=${carga} " >> ${nome}.dat echo " ${nome}" >> ${nome}.dat echo " " >> ${nome}.dat j=1 while [ ${j} -le ${m} ] do i=1 while [ ${i} -le ${n} ] do x1=`echo "scale=10;${tx} + ${ra}*c(${te} + ${inc1})"|bc -l ` #coord x1 y1=`echo "scale=10;${ty} + ${ra}*s(${te} + ${inc1})"|bc -l ` #coord y1 x2=`echo "scale=10;${tx} + ${ra}*c(${te} + ${inc2})"|bc -l ` #coord x2 y2=`echo "scale=10;${ty} + ${ra}*s(${te} + ${inc2})"|bc -l ` #coord y2 echo "${atomo1} ${x1} 1 ${y1} 1 ${z2} 1 " >> ${nome}.dat echo "${atomo2} ${x2} 1 ${y2} 1 ${D2} 1 " >> ${nome}.dat te=` echo "scale=10;${te} + ${dte}"|bc -l ` https://revista.iq.unesp.br/index.php/ecletica https://doi.org/10.26850/1678-4618eqj.v47.1SI.2022.p57-62 Supplementary Information revista.iq.unesp.br 59 Eclética Química Journal, vol. 47, special issue 1, 2022, 57-62 ISSN: 1678-4618 DOI: 10.26850/1678-4618eqj.v47.1SI.2022.p57-62 i=` expr ${i} + 1 ` done z2=` echo "scale=10;${z2} + ${D3}"|bc -l ` D2=` echo "scale=10;${D2} + ${D3}"|bc -l ` inc1=` echo "scale=10;${inc1} + ((-1)^(${j}-1))*${incte}"|bc -l ` inc2=` echo "scale=10;${inc2} + ((-1)^(${j}-1))*${incte}"|bc -l ` j=` expr ${j} + 1 ` done #rodar-mopac2016.sh ${nome}.dat #/opt/mopac/MOPAC2016.exe ${nome}.dat conv-xyz-dat-gjf-supercomputador.sh ${nome} ${metodoAb} ${baseAb} ${cargaAb} ${multiAb} 14 24 # conv-arc-dat-gjf.sh ${nome} ${metodoAb} ${baseAb} ${cargaAb} ${multiAb} # echo "batg03-vulc ${nome} " >> fila-abinitio-varredor.sh # batg03-vulc ${nome} # grep -H "SCF Done" ${nome}.log >> energias-abi-varredor.sh else #Crescimento BARCO n=` echo "${n0}"|bc -l ` #numero de carbono vezes quatro nome=nano${tipo}-${atomo1}${atomo2}-n${n}-m${m}-${metodo}-${multi}- c${carga} te=` echo "scale=10;0.0000*(2*${pi}/${n})"|bc -l ` # angulo te0=` echo "scale=10;2*${pi}/${n}"|bc -l ` # angulo incte=` echo "scale=10;${pi}/${n}"|bc -l ` #incremento do angulo de nivel dte=` echo "scale=10;(2*${pi}/${n})"|bc -l ` #incremento do angulo maior - Zn-Zn D1=`echo "scale=10;${fatd1}*(2*(${d} + ${d}*c(2*${pi}/${n})))"|bc -l ` # distancia basica do BARCO ra=`echo "scale=10;(${D1})/(sqrt(2 - 2*c(2*${pi}/${n})))"|bc -l ` #raio BARCO #curv=`echo "scale=10;1/${ra}"|bc -l ` # curvatura BARCO #echo "curv=${curv}" inc=0.00000 dte1=` echo "scale=10;${fatd2}*(${te0}/3)"|bc -l ` #incremento do angulo menor - Zn-O D3=`echo "scale=10;${fatd3}*(${d}*s(${pi}/3))"|bc -l ` # incr em z2*fatdz2 dz1=`echo "scale=10;${d}*s(${pi}/3)"|bc -l ` # incremento em z1 #dz2=`echo "scale=10;${fatdz2}*(2*${d}*s(${pi}/3))"|bc -l ` # incr em z2*fatdz2 tx=`echo "scale=10;-${ra}*c(${te} + ${inc})"|bc -l ` #translacao em x ty=`echo "scale=10;-${ra}*s(${te} + ${inc})"|bc -l ` #translacao em y z1=`echo "scale=10;0.0000*s(${pi}/6)"|bc -l ` #coord z1 # echo " ${metodo} PREC SHIFT1000 DEBUG LET T=1999999 + " > ${nome}.dat # echo " DUMP=250000 XYZ PL GEO-OK ${multi} CHARGE=${carga} " >> ${nome}.dat echo " ${metodo} UHF CYCLES=30000 PREC SHIFT1000 DEBUG LET T=19999999 + " > ${nome}.dat echo " DUMP=250000 AUX GNORM=0.01 PL GEO-OK ${multi} CHARGE=${carga} " >> ${nome}.dat echo " ${nome}" >> ${nome}.dat echo " " >> ${nome}.dat https://revista.iq.unesp.br/index.php/ecletica https://doi.org/10.26850/1678-4618eqj.v47.1SI.2022.p57-62 Supplementary Information revista.iq.unesp.br 60 Eclética Química Journal, vol. 47, special issue 1, 2022, 57-62 ISSN: 1678-4618 DOI: 10.26850/1678-4618eqj.v47.1SI.2022.p57-62 j=1 while [ ${j} -le ${m} ] do i=1 while [ ${i} -le ${n} ] do x1=`echo "scale=10;${tx} + ${ra}*c(${te} + ${inc})"|bc -l ` #coord x1 y1=`echo "scale=10;${ty} + ${ra}*s(${te} + ${inc})"|bc -l ` #coord y1 x2=`echo "scale=10;${tx} + ${ra}*c(${te} + ${dte1} + ${inc})"|bc -l ` #coord x2 y2=`echo "scale=10;${ty} + ${ra}*s(${te} + ${dte1} + ${inc})"|bc -l ` #coord y2 echo "${atomo1} ${x1} 1 ${y1} 1 ${z1} 1 " >> ${nome}.dat echo "${atomo2} ${x2} 1 ${y2} 1 ${z1} 1 " >> ${nome}.dat te=` echo "scale=10;${te} + ${dte}"|bc -l ` #z1=` echo "scale=10;${z1} + ((-1)^${i})*${dz1}"|bc -l ` i=` expr ${i} + 1 ` done z1=` echo "scale=10;${z1} + ${D3}"|bc -l ` inc=` echo "scale=10;${inc} + ((-1)^(${j}))*${incte}"|bc -l ` j=` expr ${j} + 1 ` done #!/bin/bash #adiçao de hidrogenio nas pontas de nanobar #Msc.Jeziel e Dr.José Divino dos Santos v.01 23/08/2018 nome=$1 #nomes dos arquivos bar.mol (sem .mol) tipo=$2 #tipo de nanotubos: 1-armchair 2-zigzag if [ ${tipo} -eq 1 ] then ###Armchair echo > temp1; rm temp1; echo > temp2; rm temp2; n=` echo ${nome}.mol|cut - d- -f3|cut -dn -f2 `; m=` echo ${nome}.mol|cut -d- -f4|cut -dm -f2 `; nat=` echo "2*${n}*${m}"|bc `; nf=` echo "2*${n}*(${m} - 1) + 2"|bc ` ;nu=` echo "2*${n} + 2"|bc `;nl=` expr ${nat} + 2 `; i=3; while [ ${i} -le ${nl} ];do v=(` head -${i} ${nome}.mol|tail -1|awk '{printf("%s %6.6f %6.6f %6.6f \n", $1, $2, $3, $4 )}'`); if [ ${i} -le ${nu} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; awk -v vx="${v[1]}" -v vy="${v[2]}" -v vz="${v[3]}" 'BEGIN{printf("%s %6.6f %6.6f %6.6f \n", "H", vx, vy, vz - 1.0)}' >> temp2 ; fi ; if [ ${i} -gt ${nu} ] && [ ${i} -le ${nf} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; fi; if [ ${i} -gt ${nf} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; awk -v vx="${v[1]}" -v vy="${v[2]}" -v vz="${v[3]}" 'BEGIN{printf("%s %6.6f %6.6f %6.6f \n", "H", vx, vy, vz + 1.0)}' >> temp2 ; fi ; i=` expr ${i} + 1 ` ; done ; natH=` echo "4*${n}"|bc ` ; natotal=` echo "2*${n}*${m} + ${natH}"|bc `; echo " ${natotal} " > ${nome}-${natH}H.mol ; echo " https://revista.iq.unesp.br/index.php/ecletica https://doi.org/10.26850/1678-4618eqj.v47.1SI.2022.p57-62 Supplementary Information revista.iq.unesp.br 61 Eclética Química Journal, vol. 47, special issue 1, 2022, 57-62 ISSN: 1678-4618 DOI: 10.26850/1678-4618eqj.v47.1SI.2022.p57-62 ">> ${nome}-${natH}H.mol; cat temp1 temp2 >> ${nome}-${natH}H.mol; molden ${nome}-${natH}H.mol else ###Zigzag #rm temp1; echo > temp2; rm temp2; n=` echo ${nome}.mol|cut -d- -f3|cut - dn -f2 `; m=` echo ${nome}.mol|cut -d- -f4|cut -dm -f2 `; nat=` echo "2*${n}*${m}"|bc `; nf=` echo "2*${n}*(${m} - 1) + 2"|bc ` ;nu=` echo "2*${n} + 2"|bc `;nl=` expr ${nat} + 2 `; i=3; while [ ${i} -le ${nl} ];do v=(` head -${i} ${nome}.mol|tail -1|awk '{printf("%s %6.6f %6.6f %6.6f \n", $1, $2, $3, $4 )}'`); if [ ${i} -le ${nu} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; awk -v vx="${v[1]}" -v vy="${v[2]}" -v vz="${v[3]}" -v i0="${i}" 'BEGIN{ip=(-1)^(i0); if(ip==-1){ printf("%s %6.6f %6.6f %6.6f \n", "H", vx, vy, vz - 1.0); }; }' >> temp2 ; fi ; if [ ${i} -gt ${nu} ] && [ ${i} -le ${nf} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; fi; if [ ${i} -gt ${nf} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; awk -v vx="${v[1]}" -v vy="${v[2]}" -v vz="${v[3]}" -v i0="${i}" 'BEGIN{ ip=(-1)^(i0); if(ip==1){ printf("%s %6.6f %6.6f %6.6f \n", "H", vx, vy, vz + 1.0); }; }' >> temp2 ; fi ; i=` expr ${i} + 1 ` ; done ; natH=` echo "2*${n}"|bc ` ; natotal=` echo "2*${n}*${m} + ${natH}"|bc `; echo " ${natotal} " > ${nome}-${natH}H.mol ; echo " ">> ${nome}-${natH}H.mol; cat temp1 temp2 >> ${nome}-${natH}H.mol; molden ${nome}-${natH}H.mol echo > temp1; rm temp1; echo > temp2; rm temp2; echo > temp3; rm temp3; n=` echo ${nome}.mol|cut -d- -f3|cut -dn -f2 `; m=` echo ${nome}.mol|cut -d- -f4|cut -dm -f2 `; nat=` echo "2*${n}*${m}"|bc `; meio=` echo "${n}*${m}"|bc `; nf=` echo "2*${n}*(${m} - 1) + 2"|bc ` ;nu=` echo "2*${n} + 2"|bc `;nl=` expr ${nat} + 2 `; i=3; while [ ${i} -le ${nl} ];do v=(` head -${i} ${nome}.mol|tail -1|awk '{printf("%s %6.6f %6.6f %6.6f \n", $1, $2, $3, $4 )}'`); if [ ${i} -le ${nu} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; awk -v vx="${v[1]}" -v vy="${v[2]}" -v vz="${v[3]}" -v i0="${i}" 'BEGIN{ip=(-1)^(i0); if(ip==-1){ printf("%s %6.6f %6.6f %6.6f \n", "H", vx, vy, vz - 1.0); }; }' >> temp2 ; fi ; if [ ${i} -gt ${nu} ] && [ ${i} -le ${nf} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; fi; if [ ${i} -gt ${nf} ]; then echo "${v[0]} ${v[1]} ${v[2]} ${v[3]}" >> temp1 ; awk -v vx="${v[1]}" -v vy="${v[2]}" -v vz="${v[3]}" -v i0="${i}" 'BEGIN{ ip=(-1)^(i0); if(ip==1){ printf("%s %6.6f %6.6f %6.6f \n", "H", vx, vy, vz + 1.0); }; }' >> temp2 ; fi ; if [ ${i} -eq ${meio} ]; then awk -v vx="${v[1]}" -v vy="${v[2]}" -v vz="${v[3]}" 'BEGIN{ printf("%s %6.6f %6.6f %6.6f \n", "C", vx + 1.70 , vy , vz ); }' >> temp3 ; fi ; i=` expr ${i} + 1 ` ; done ; natH=` echo "2*${n}"|bc ` ; natotal=` echo "2*${n}*${m} + ${natH} + 1"|bc `; echo " ${natotal} " > ${nome}-${natH}H.mol ; echo " ">> ${nome}-${natH}H.mol; cat temp1 temp2 temp3 >> ${nome}-${natH}H.mol; molden ${nome}-${natH}H.mol fi https://revista.iq.unesp.br/index.php/ecletica https://doi.org/10.26850/1678-4618eqj.v47.1SI.2022.p57-62 Supplementary Information revista.iq.unesp.br 62 Eclética Química Journal, vol. 47, special issue 1, 2022, 57-62 ISSN: 1678-4618 DOI: 10.26850/1678-4618eqj.v47.1SI.2022.p57-62 S2. script to encapsulate the BNZ in the geometric center of the BNNT and CNT models. #!/bin/bash #Ponto geométrico #MsC. Jeziel Rodrigues dos Santos 28/03/2019 v.01 nome=$1 #nome do arquivo.mol (sem .mol) nl=` wc -l ${nome}.mol|awk '{print $1}' ` nat=` wc -l ${nome}.mol|awk '{print $1 - 2}' ` #######ponto médio coordenada x i=3; sx=0.000000; while [ ${i} -le ${nat} ] do at=` head -${i} ${nome}.mol|tail -1|awk '{print $1}' ` x=` head -${i} ${nome}.mol|tail -1|awk '{print $2}' ` sx=` echo "scale=6;${sx} + ${x}"|bc -l ` #echo "${at} ${x} ${sx}" i=` expr ${i} + 1 ` done mx=` echo "scale=6;${sx}/${nat}"|bc -l ` #echo [ mediax=${mx} ] #######ponto médio coordenada y i=3; sy=0.000000; while [ ${i} -le ${nat} ] do at=` head -${i} ${nome}.mol|tail -1|awk '{print $1}' ` y=` head -${i} ${nome}.mol|tail -1|awk '{print $3}' ` sy=` echo "scale=6;${sy} + ${y}"|bc -l ` #echo "${at} ${y} ${sy}" i=` expr ${i} + 1 ` done my=` echo "scale=6;${sy}/${nat}"|bc -l ` #echo [ mediax=${my} ] #######ponto médio coordenada z i=3; sz=0.000000; while [ ${i} -le ${nat} ] do at=` head -${i} ${nome}.mol|tail -1|awk '{print $1}' ` z=` head -${i} ${nome}.mol|tail -1|awk '{print $3}' ` sz=` echo "scale=6;${sz} + ${z}"|bc -l ` #echo "${at} ${z} ${sz}" i=` expr ${i} + 1 ` done mz=` echo "scale=6;${sz}/${nat}"|bc -l ` echo [${mx} ${my} ${mz} ] > ponto-medio-${nome}.mol https://revista.iq.unesp.br/index.php/ecletica https://doi.org/10.26850/1678-4618eqj.v47.1SI.2022.p57-62