NBO介紹要點課件

NaturalBondOrbital(NBO)EthaneC-Cbondin1,2,and3dimensionsNaturalBondOrbital(NBO)Etha1NaturalBondOrbital(NBO)Etha1.NBO概念、理論基本思想2.NBO程序介紹3.Gaussian&ADF中NBO功能的使用4.NBOVIEW程序介紹1.NBO概念、理論基本思想21.NBO概念、理論基本思想1.NBO概念、理論基本思想21.NBO概念、理論基本思想任何量子化學(xué)中，對指定電荷在空間內(nèi)不同區(qū)域分布的劃分方案關(guān)鍵是定義分子中的原子子空間。量子化學(xué)研究的一個重要的對象就是多原子分子體系中各原子的電子組態(tài)和靜電荷分布，分子中的原子電荷分布對于從化學(xué)的角度去解釋分子波函數(shù)，理解化學(xué)變化的內(nèi)在本質(zhì)有十分重要的作用。但是對于原子電荷和軌道的電荷密度布居進(jìn)行定量的量子化學(xué)計算時，即使使用精確的基組函數(shù),往往難以得到滿意的結(jié)果。1.NBO概念、理論基本思想任何量子化學(xué)中，對指定電荷在空間31.NBO概念、理論基本思想任何量子化學(xué)中，對指定電荷在空間自然鍵軌道分析（NaturalBondOrbitalanalysis）是由AlanE.Reed,WeinstockandWeinhold在1984年提出的作為研究多原子分子體系中的雜化和共價效應(yīng)的方法。與傳統(tǒng)的Mülliken布居分析方法相比，自然鍵軌道分析方法受L?wdin的對稱轉(zhuǎn)換思想啟發(fā)，采用正交的矩陣去避免結(jié)果的無實際意義的負(fù)軌道占據(jù)值。因而自然鍵軌道分析方法在描繪電子組態(tài)和原子上的靜電荷方面的計算結(jié)果與實驗結(jié)果更加吻合。NBO對HF、相關(guān)波函數(shù)及DFT方法均適用。自然鍵軌道分析4自然鍵軌道分析自然鍵軌道分析4自然鍵軌道是局域的少中心軌道（通常典型的為1或2，偶爾更多），在理想的緊湊形式下，描述電子對路易斯類似的分子成鍵模式（或在開殼情況下為單獨的電子）。更確切的說，NBOs是一系列正交化的局域“最大占據(jù)”軌道，其包含的N/2部分（或在開殼情況下的N部分）給出總的N電子密度最精確可能的路易斯類似描述。自然鍵軌道是局域的少中心軌道（通常典型的為1或2，偶爾更多）5自然鍵軌道是局域的少中心軌道（通常典型的為1或2，偶爾更多）

NBOs由NHOs{hA}組成，每個都形成一個優(yōu)化的在指定中心的NAOs線性組合hA=Σk

akΘk(A)與NAOs類似，NHOs形成一個遍及整個基本空間的完全的正交化系列。核NBOs（在NBO輸出中標(biāo)記為“CR”)典型幾乎為純的NAO特征。單中心的“孤對”（非鍵）NBOsnA（在NBO輸出中標(biāo)記為“LP”）各自由一個單獨的規(guī)范NHO組成nA=hA

NBOs由NHOs{hA}組成，每個都形成一個優(yōu)化的在指6

NBOs由NHOs{hA}組成，每個都形成一個優(yōu)化的在指雙中心鍵NBOsΩAB(在NBO輸出中標(biāo)記為“BD”)為兩個成鍵NHOshA,hB線性組合形成，對應(yīng)于經(jīng)典的Mulliken和Lennard-Jones鍵軌道形式，

ΩAB=aAhA+aBhB

其極化系數(shù)aA,aB滿足aA2+aB2=1。依據(jù)這些系數(shù)值，一個成鍵NBO可能處于共價(aA=aB)和離子(aA>>aB)鍵限度之間。然而，在高極化形式(aA>>aB)的雙中心ΩAB和單中心nA(aA=1,aB=0)之間沒有明顯的區(qū)別。為了與一般化學(xué)用法一致，只要在一個單中心上的電子密度達(dá)到95%或更多時(aA2≥0.95)，NBO程序確定一個高極化ΩAB為孤對nA。雙中心鍵NBOsΩAB(在NBO輸出中標(biāo)記為“BD”)7雙中心鍵NBOsΩAB(在NBO輸出中標(biāo)記為“BD”)每一項NBO中，價層雜化hA,hB必須由相應(yīng)的外部的反鍵NBOΩ*AB(在NBO輸出中標(biāo)記為“BD*”)正交地補充。

Ω*AB=aBhA?aAhB

價層反鍵Ω*AB為非路易斯類型，在基態(tài)的NLS描述中沒有作用，特別項“antibond”反鍵源自相同產(chǎn)生成鍵NBOs的未充滿價基雜化，因此Ω*AB's代表相應(yīng)原子未用的價層容量，未被共價形式飽和。Ω*AB's被發(fā)現(xiàn)是典型的最重要的非路易斯"acceptor"軌道，對共振穩(wěn)定性、分子間氫鍵和其他形式的超分子給體－受體結(jié)合起貢獻(xiàn)。可得到的Ω*AB形狀和能量知識是理解超出理想的路易斯結(jié)構(gòu)描述的重要的"非共價"和"離域"現(xiàn)象的關(guān)鍵。每一項NBO中，價層雜化hA,hB必須由相應(yīng)的外部的8每一項NBO中，價層雜化hA,hB必須由相應(yīng)的外部的價基非路易斯NBOs{Ω*AB}被一系列"Rydberg-type"單中心NBOsrA（在程序輸出中標(biāo)價為"RY*"）所補充使NBO基礎(chǔ)完善。與額外價NAOs來源類似，這些NBOs顯然有可忽略的占據(jù)，因為考慮化學(xué)的目的能夠被忽略。因此，顯著占據(jù)的NBOs的有效延伸減至NAOs的NMB部分，與化學(xué)知識一致。價基非路易斯NBOs{Ω*AB}被一系列"Rydberg-9價基非路易斯NBOs{Ω*AB}被一系列"Rydberg-

2.NBO程序介紹KeywordParms?KeywordDescriptionAOINFONWriteAObasisinformationtoLFN31ARCHIVEOWriteARCHIVE(FILE47)forstand-aloneGENNBOinputBNDIDXNNAO-WibergBondIndexandrelatedvalencyindicesFILEYSpecifyfilestemforPLOTfilesPLOTNWritefilesfororbitalplotting

3CBONDNSearchfor3-centerNBOs

ControlOptions2.NBO程序介紹KeywordPar102.NBO程序介紹KeywordParMainProgramOptions

KeywordParms?

KeywordDescription

Page

[BEND]O.Hybriddirectionalityand"bond-bending"analysisCMOO.BondingcharacterofcanonicalmolecularorbitalsDIPOLEO.Dipolemomentanalysis[E2PERT]O.2nd-orderperturbativeestimatesofNBOinteractionsNBBPO.Naturalbond-bondpolarizabilityindices[NBO]NNaturalbondorbitalcompositions[NBOSUM]N.NBOsummarytableNCSO.NaturalchemicalshieldinganalysisNJCO.NaturalJ-couplinganalysisNLMONNaturallocalizedmolecularorbitalcompositions[NPA]NNaturalpopulationanalysisNRTNNaturalresonancetheoryanalysisSTERICO.Naturalstericanalysis3CHBN3-c,4-ehyperbondsearchKeywordsinbracketsdenote[default]optionsthatareperformedevenifthe$NBOkeylistisempty.Notethatsomeoptionsautomaticallyturnonotherkeywordsthatareneededtoperformtheanalysis(e.g.,NLMOisautomaticallyturnedonforDIPOLE,NCS,orNJCanalysis).Usethevariouscontroloptionkeywords(suchasthePRINTorthresholdkeywords)tofurthercontroloutputfromeachmainprogramoption.

MainProgramOptionsKeywo11MainProgramOptionsKeywoNBOTranslatesAccurateCalculationsIntoChemicalInsightsChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…NBOTranslatesAccurateCalcul12NBOTranslatesAccurateCalculNaturalPopulationAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…SummaryofNaturalPopulationAnalysis: NaturalPopulation NaturalAtom# ChargeCoreValenceRydbergTotalC1 -0.440791.999004.438480.003316.44079N2 -0.897151.999535.893780.003847.89715H3 0.183700.000000.814530.001770.81630H4 0.217130.000000.781920.000960.78287H5 0.217130.000000.781920.000960.78287H6 0.359990.000000.638790.001220.64001H7 0.359990.000000.638790.0012 0.64001=======================================================================*Total* 0.000003.9985313.988200.0132818.00000****SampleOutput****thenaturalpopulationsaresummarizedasaneffectivevalenceelectronconfiguration("naturalelectronconfiguration")foreachatom:Atom#NaturalElectronConfigurationC1[core]2s(1.09)2p(3.35)N2[core]2s(1.43)2p(4.47)H31s(0.81)H41s(0.78)H51s(0.78)H61s(0.64)H71s(0.64)NaturalPopulationAnalysisCha13NaturalPopulationAnalysisChaNATURALBONDORBITALS(Summary): PrincipalDelocalizationsNBO Occupancy Energy (geminal,vicinal,remote)=======================================================================Molecularunit1(CH3NO)1.BD(1)H1-N3 1.99309 -0.89250 32(v),20(v)2.BD(1)H2-N3 1.99322 -0.87920 3(v),19(v),32(v),21(v)3.BD(1)N3-C4 1.99828 -1.10527 29(g),28(g)4.BD(1)C4-O5 1.99925 -0.50592 31(g),16(v)5.BD(2)C4-O5 1.99802 -1.40674 19(g),28(v)6.BD(1)C4-H6 1.98929 -0.75792 29(v),23(v),15(v)7.CR(1)N3 1.99922 -15.31924 20(v),19(v),13(v),14(v)8.CR(1)C4 1.99939 -11.16963 27(v),29(v),28(v)9.CR(1)O5 1.99963 -20.09206 19(v),25(g),20(v)10.LP(1)N3 1.80683 -0.39458 31(v),22(v11.LP(1)O5 1.98262 -0.93620 19(v),20(v),33(v),30(v) 29(r)12.LP(2)O5 1.88568 -0.40982 30(v),33(v),20(v)****SampleOutput****NBOSummaryChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…NATURALBONDORBITALS(Summary14NATURALBONDORBITALS(Summary1.H1-N3?NBOType

N-Hsigmabond

?HybridComposition

0.5390(s)H+0.8423(sp2.23)N?Occupancy

1.99309

e

NaturalBondOrbitalAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…(Occupancy)Bondorbital/Coefficients/Hybrids1.(1.99309)BD(1)H1-N3 (29.05%)0.5390*H1s(100.00%) -1.0000-0.0010 (70.95%)0.8423*N3s(30.92%)p2.23(69.08%) 0.0002-0.5561-0.00200.68790.0155 -0.46600.0088-0.00010.00002.(1.99322)BD(1)H2-N3 (28.52%)0.5341*H2s(100.00%) -1.0000-0.0043 (71.48%)0.8454*N3s(30.20%)p2.31(69.80%) 0.0001-0.5495-0.00090.11580.0158 0.82730.00520.00000.0000****SampleOutput****1.H1-N3NaturalBondOrbitalA151.H1-N3NaturalBondOrbitalA(Occupancy)Bondorbital/Coefficients/Hybrids1.(1.99309)BD(1)H1-N3 (29.05%)0.5390*H1s(100.00%) -1.0000-0.0010 (70.95%)0.8423*N3s(30.92%)p2.23(69.08%) 0.0002-0.5561-0.00200.68790.0155 -0.46600.0088-0.00010.00002.(1.99322)BD(1)H2-N3 (28.52%)0.5341*H2s(100.00%) -1.0000-0.0043 (71.48%)0.8454*N3s(30.20%)p2.31(69.80%) 0.0001-0.5495-0.00090.11580.0158 0.82730.00520.00000.0000****SampleOutput****1.H1-N3?NBOType

N-Hsigmabond

?HybridComposition

0.5390(s)H+0.8423(sp2.23)N?Occupancy

1.99309e

NaturalBondOrbitalAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…(Occupancy)Bondorbital/Coef16(Occupancy)Bondorbital/CoefBondOrdersChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…1.241.001.79NaturalBondOrder:(total/covalent/ionic)Atom123456

1.Ht0.00200.00000.99590.00000.00000.0000c0.00000.57870.00000.00000.0000i0.00000.41720.00000.00000.00002.Ht0.00000.00500.99280.00000.00000.0000c0.00000.56640.00000.00000.0000i0.00000.42650.00000.00000.00003.Nt0.99590.99280.76911.24220.00000.0000c0.57870.56640.75190.00000.0000i0.41720.42650.49030.00000.00004.Ct0.00000.00001.24220.00001.79040.9674c0.00000.00000.75191.09670.7956i0.00000.00000.49030.69370.17195.Ot0.00000.00000.00001.79042.20760.0000c0.00000.00000.00001.09670.0000i0.00000.00000.00000.69370.00006.Ht0.00000.00000.00000.96740.00000.0275c0.00000.00000.00000.79560.0000i0.00000.00000.00000.17190.0000****SampleOutput****H1-N3:0.58Covalent+0.42Ionic=1.00TotalN3-C4:0.75Covalent+0.49Ionic=1.24TotalC4-O5:1.10Covalent+0.69Ionic=1.79TotalBondOrdersCharges1.241.001.7917BondOrdersCharges1.241.001.79WibergbondindexWibergbondindexmatrixintheNAObasis:Atom1234567

1.C0.00000.94030.94030.94280.99820.00220.00222.H0.94030.00000.00110.00050.00550.00050.00723.H0.94030.00110.00000.00050.00550.00720.00054.H0.94280.00050.00050.00000.02580.00010.00015.N0.99820.00550.00550.02580.00000.85640.85646.H0.00220.00050.00720.00010.85640.00000.00037.H0.00220.00720.00050.00010.85640.00030.0000****SampleOutput****WibergbondindexWibergbondi18WibergbondindexWibergbondiPerturbationTheoryEnergyAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…SECONDORDERPERTURBATIONTHEORYANALYSISOFFOCKMATRIXINNBOBASISThresholdforprinting:0.50kcal/mol E(2)E(j)-E(i)F(i,j)DonorNBO(i) AcceptorNBO(j) kcal/mola.u.a.u.==========================================================================withinunit11.BD(1)H1-N3 20.RY*(2)C4 2.541.890.0621.BD(1)H1-N3 32.BD*(2)C4-O5 4.411.740.0782.BD(1)H2-N3 19.RY*(1)C4 2.101.760.0542.BD(1)H2-N3 21.RY*(3)C4 0.592.320.0332.BD(1)H2-N3 32.BD*(2)C4-O5 1.281.720.0422.BD(1)H2-N3 33.BD*(1)C4-H6 2.451.530.0553.BD(1)N3-C4 28.BD*(1)H1-N3 0.641.760.0303.BD(1)N3-C4 29.BD*(1)H2-N3 0.711.760.0324.BD(1)C4-O5 16.RY*(2)N3 0.891.900.0374.BD(1)C4-O5 31.BD*(1)C4-O5 0.950.670.0245.BD(2)C4-O5 19.RY*(1)C4 1.832.290.0585.BD(2)C4-O5 28.BD*(1)H1-N3 1.592.060.0516.BD(1)C4-H6 15.RY*(1)N3 0.652.810.0386.BD(1)C4-H6 23.RY*(1)O5 1.612.790.0606.BD(1)C4-H6 29.BD*(1)H2-N3 5.241.420.077****SampleOutput****(C4-H6)*(H2-N3)stabilization5.24kcal/mol(2ndorderestimate)PerturbationTheoryEnergyAna19PerturbationTheoryEnergyAnaNaturalChemicalShielding(NCS)Analysis

ChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…NaturalNMRChemicalShieldingTensorAnalysisNCSTensoranalysisisusing 8624wordsThresholdforprinting:0.10ppmSummaryofisotropicNMRchemicalshieldingTotalLewis(L)andnon-Lewis(NL)contributions:(ppm)NBO C(1)N(2)H(3)H(4)H(5)H(6)H(7)

1.C1-N2L-6.546.390.560.500.502.412.41NL0.17-0.350.030.080.08-0.09-0.092.C1-H3L-4.210.5026.521.851.850.100.10NL-0.61-0.390.07-0.05-0.05-0.01-0.013.C1-H4L-2.642.112.1025.732.040.130.21NL-0.21-1.42-0.010.050.04-0.04-0.084.C1-H5L-2.642.112.102.0425.730.210.13NL-0.21-1.42-0.010.040.05-0.08-0.045.N2-H6L0.097.190.340.290.2422.873.36NL-0.010.17-0.02-0.12-0.010.03-0.04****SampleOutput****The(C1-N2)bondde-shieldsthecarbonby6.54ppmandshieldsthenitrogenby6.39ppm.NaturalChemicalShielding(NC20NaturalChemicalShielding(NCNaturalResonanceTheory(NRT)Improvements

ChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore… ResonanceRS Weight(%) Added(Removed)1*(2) 69.362* 24.39 N3-C4,(C4-O5),(N3),O53 2.37 (N3-C4),C4-O5,N3,(O5)4(2) 1.99 C4-O5,(C4-H6),(O5),H65(2) 0.76 N3-C4,(C4-H6),(N3),H66 0.36 (H2-N3),N3-C4,(C4-H6),H27 0.16 (H1-N3),N3-C4,(C4-O5),O58 0.15 (H2-N3),N3-C4,(C4-O5),O59 0.14 (H1-N3),N3-C4,(C4-O5),H110 0.14 (H2-N3),N3-C4,N3-C4,(C4-O5), (C4-H6),H2,(N3),O511-15 0.17100.00*Total* [*=referencestructure]****SampleOutput****Togetthe2ndresonancestructurefromthe1st:

AddabondbetweenN3andC4

RemoveabondbetweenC4andO5

RemovealonepaironN3andaddalonepairtoO5NaturalResonanceTheory(NRT)21NaturalResonanceTheory(NRT)NewFeaturesinNBO5.0CanonicalMolecularOrbital(CMO)Analysis

NaturalChemicalShielding(NCS)Analysis

NaturalJ-Coupling(NJC)Analysis

3-center,4-eHyperbond(3CHB)Search

LargerSystems(999atoms，9999basisfunctionatmost,200atoms,2000basisfunctionindefault)NaturalResonanceTheory(NRT)Improvements

NaturalLocalizedMolecularOrbital(NLMO)Improvements

STERICImprovement

NewCheckpointingOptions

NewMatrixOutputOptions

TransitionMetalHybridDirectionality

BasisLinearDependencyDetection/Protection

NewPC-WindowsGENNBOStand-AloneVersion

/~nbo5/

NewFeaturesinNBO5.0Canonic22NewFeaturesinNBO5.0Canonic3.NBO-AffiliatedElectronicStructureSystems

andProtectedInterfacesSystem(*)Vendor/DistributorJaguar

(1)Schrodinger,Inc.Q-Chem(1)Q-Chem,Inc.PQS(1)ParallelQuantumSystemsNWChem(1)PacificNorthwestNationalLaboratoriesADF(1)ScientificComputing&ModellingN.V.PCGAMESS(2)AlexA.Granovsky,MoscowStateUniversityGAMESS(U.S.)(3)AmesLaboratories,IowaStateUniversityGaussian98/03(4)Gaussian,Inc.(1)NBO5.0is/willbeincluded.(2)NBO5.0included,butrequiresNBOpasswordfromTCI/NBOSoftware(3)Protectedinterface;requireslinkingtoNBO5.0fromTCI/NBOSoftware.(4)NBO3.1included,butcanbeupgradedwithNBO5.0fromTCI/NBOSoftware.3.NBO-AffiliatedElectronicS233.NBO-AffiliatedElectronicSAdfnbo,gennbo:NBOanalysisGENNBO-supportedoptionsincludeallkeywordsexceptthoseexplicitlyrequiringinteractivecommunicationwiththehostelectronicstructuresystem(viz.,$DELdeletions,NEDA,NCS,NJC).GENNBO"communicates"withtheoriginalADFcalculationthroughanarchivefile(JOB.47file,preservingallnecessarydetailsofthefinaldensity)thatisinitiallygeneratedbyADFandsubsequentlybecomestheinputfileforGENNBO.NBOinADFAdfnbo,gennbo:NBOanalysisGE24Adfnbo,gennbo:NBOanalysisGEFULLFOCKAOMAT2FILESAVETAPE15EndInputEor$ADFBIN/adfnbo<<eor調(diào)用nbo模塊eorecho""echo""echo"ContentsofFILE47="echo""echo""catFILE47$ADFBIN/gennbo<FILE47產(chǎn)生。47文件作為進(jìn)一步nbo分析的輸入文件echo""echo""echo"Contentsofnbotmp.37="echo""echo""catnbotmp.37echo""echo""echo"Contentsofnbotmp.39="echo""echo""catnbotmp.39echo""echo""echo"Contentsofnbotmp.49="echo""echo""catnbotmp.49FULLFOCK25FULLFOCKFULLFOCK25NBOinGaussianGaussian包含鏈接為607的程序NBOVersion3.1NBO的大小是200個原子和10000個基函數(shù)。NBO輸入Pop=NBO

Pop=NBOReadNBOinGaussianGaussian包含鏈接為6026NBOinGaussianGaussian包含鏈接為60input#phf/3-21gpop(nboread)

ch3nh2nbo

01…….$nbobndidxarchive$endinput#phf/3-21gpop(nboread)27input#phf/3-21gpop(nboread)iPopulationNBO有關(guān)選項NBO使用NBO版本3，進(jìn)行完全的自然鍵軌道分析。NPA

只執(zhí)行NBO的自然布居分析階段。NBORead進(jìn)行完全的NBO分析，使用從輸入讀入的數(shù)據(jù)控制分析計算。使用這個關(guān)鍵字用于指定NBO版本4和5。NBODel進(jìn)行刪除某些相互作用預(yù)測其影響的NBO分析。只適用于SCF方法。SaveNBOs,SaveNLMOs,SaveMixed把自然鍵軌道，自然局域化分子軌道，占據(jù)軌道的NBO和非占據(jù)軌道的NLMO保存在checkpoint文件中(以后用于可視化程序顯示)。PopulationNBO有關(guān)選項28PopulationNBO有關(guān)選項PopulationNBNBOProgramsandInterfacesforHostElectronicStructureSystems(ESS)NBOProgramsandInterfacesfo29NBOProgramsandInterfacesfo4.NBOView:NBOOrbitalGraphicsPlotter

TheNBOViewprogramcreatesgraphical1D/2D/3DimagesofelectronicorbitalsproducedbytheNaturalBondOrbital(NBO)program.$NBOPLOTFILE=ch3nh2$END4.NBOView:NBOOrbitalGraphi304.NBOView:NBOOrbitalGraphiNBOViewOperationTheNBOprogramproducesaseriesof"plotfiles“(say,ch3nh2.31,ch3nh2.32,...,ch3nh2.46)thatcanbereadbyNBOViewtoproducegraphicallocalizedanddelocalizedorbitalimagesforthechosenmolecule.NBOViewOperationTheNBOprogr31NBOViewOperationTheNBOprogrNBOViewCommands

BasisSelectsthecurrentbasissetCOntourDisplays2DcontoursPRofileDisplaysa1DorbitalDensityDisplayscontoursoftotalelectrondensitySHow

s1,s2,...Displaysthecontentsofcurrentstoragelocationss1,s2,...DRaw

s1,s2,...CreatesafilesuitableforprintingVIew

s1,s2,...Createsa3Drenderedphoto-likeviewoftheorbitalobjectsinstoragePLane

SpecifythecontourplaneVEctor

SpecifythevectoraxisforPROFILEplotsLAbel

Displaysalistoforbitallabelsforthecurrentbasisset.NBOViewCommandsBasisSe32NBOViewCommandsBasisSeExample:CH3NH2NBO4.BDC1-N5

0.6319Csp3.5+0.7751Nsp2.11Example:CH3NH2NBO4.BDC1-33Example:CH3NH2NBO4.BDC1-NaturalBondOrbital(NBO)EthaneC-Cbondin1,2,and3dimensionsNaturalBondOrbital(NBO)Etha34NaturalBondOrbital(NBO)Etha1.NBO概念、理論基本思想2.NBO程序介紹3.Gaussian&ADF中NBO功能的使用4.NBOVIEW程序介紹1.NBO概念、理論基本思想351.NBO概念、理論基本思想1.NBO概念、理論基本思想351.NBO概念、理論基本思想任何量子化學(xué)中，對指定電荷在空間內(nèi)不同區(qū)域分布的劃分方案關(guān)鍵是定義分子中的原子子空間。量子化學(xué)研究的一個重要的對象就是多原子分子體系中各原子的電子組態(tài)和靜電荷分布，分子中的原子電荷分布對于從化學(xué)的角度去解釋分子波函數(shù)，理解化學(xué)變化的內(nèi)在本質(zhì)有十分重要的作用。但是對于原子電荷和軌道的電荷密度布居進(jìn)行定量的量子化學(xué)計算時，即使使用精確的基組函數(shù),往往難以得到滿意的結(jié)果。1.NBO概念、理論基本思想任何量子化學(xué)中，對指定電荷在空間361.NBO概念、理論基本思想任何量子化學(xué)中，對指定電荷在空間自然鍵軌道分析（NaturalBondOrbitalanalysis）是由AlanE.Reed,WeinstockandWeinhold在1984年提出的作為研究多原子分子體系中的雜化和共價效應(yīng)的方法。與傳統(tǒng)的Mülliken布居分析方法相比，自然鍵軌道分析方法受L?wdin的對稱轉(zhuǎn)換思想啟發(fā)，采用正交的矩陣去避免結(jié)果的無實際意義的負(fù)軌道占據(jù)值。因而自然鍵軌道分析方法在描繪電子組態(tài)和原子上的靜電荷方面的計算結(jié)果與實驗結(jié)果更加吻合。NBO對HF、相關(guān)波函數(shù)及DFT方法均適用。自然鍵軌道分析37自然鍵軌道分析自然鍵軌道分析37自然鍵軌道是局域的少中心軌道（通常典型的為1或2，偶爾更多），在理想的緊湊形式下，描述電子對路易斯類似的分子成鍵模式（或在開殼情況下為單獨的電子）。更確切的說，NBOs是一系列正交化的局域“最大占據(jù)”軌道，其包含的N/2部分（或在開殼情況下的N部分）給出總的N電子密度最精確可能的路易斯類似描述。自然鍵軌道是局域的少中心軌道（通常典型的為1或2，偶爾更多）38自然鍵軌道是局域的少中心軌道（通常典型的為1或2，偶爾更多）

NBOs由NHOs{hA}組成，每個都形成一個優(yōu)化的在指定中心的NAOs線性組合hA=Σk

akΘk(A)與NAOs類似，NHOs形成一個遍及整個基本空間的完全的正交化系列。核NBOs（在NBO輸出中標(biāo)記為“CR”)典型幾乎為純的NAO特征。單中心的“孤對”（非鍵）NBOsnA（在NBO輸出中標(biāo)記為“LP”）各自由一個單獨的規(guī)范NHO組成nA=hA

NBOs由NHOs{hA}組成，每個都形成一個優(yōu)化的在指39

NBOs由NHOs{hA}組成，每個都形成一個優(yōu)化的在指雙中心鍵NBOsΩAB(在NBO輸出中標(biāo)記為“BD”)為兩個成鍵NHOshA,hB線性組合形成，對應(yīng)于經(jīng)典的Mulliken和Lennard-Jones鍵軌道形式，

ΩAB=aAhA+aBhB

其極化系數(shù)aA,aB滿足aA2+aB2=1。依據(jù)這些系數(shù)值，一個成鍵NBO可能處于共價(aA=aB)和離子(aA>>aB)鍵限度之間。然而，在高極化形式(aA>>aB)的雙中心ΩAB和單中心nA(aA=1,aB=0)之間沒有明顯的區(qū)別。為了與一般化學(xué)用法一致，只要在一個單中心上的電子密度達(dá)到95%或更多時(aA2≥0.95)，NBO程序確定一個高極化ΩAB為孤對nA。雙中心鍵NBOsΩAB(在NBO輸出中標(biāo)記為“BD”)40雙中心鍵NBOsΩAB(在NBO輸出中標(biāo)記為“BD”)每一項NBO中，價層雜化hA,hB必須由相應(yīng)的外部的反鍵NBOΩ*AB(在NBO輸出中標(biāo)記為“BD*”)正交地補充。

Ω*AB=aBhA?aAhB

價層反鍵Ω*AB為非路易斯類型，在基態(tài)的NLS描述中沒有作用，特別項“antibond”反鍵源自相同產(chǎn)生成鍵NBOs的未充滿價基雜化，因此Ω*AB's代表相應(yīng)原子未用的價層容量，未被共價形式飽和。Ω*AB's被發(fā)現(xiàn)是典型的最重要的非路易斯"acceptor"軌道，對共振穩(wěn)定性、分子間氫鍵和其他形式的超分子給體－受體結(jié)合起貢獻(xiàn)?？傻玫降摩?AB形狀和能量知識是理解超出理想的路易斯結(jié)構(gòu)描述的重要的"非共價"和"離域"現(xiàn)象的關(guān)鍵。每一項NBO中，價層雜化hA,hB必須由相應(yīng)的外部的41每一項NBO中，價層雜化hA,hB必須由相應(yīng)的外部的價基非路易斯NBOs{Ω*AB}被一系列"Rydberg-type"單中心NBOsrA（在程序輸出中標(biāo)價為"RY*"）所補充使NBO基礎(chǔ)完善。與額外價NAOs來源類似，這些NBOs顯然有可忽略的占據(jù)，因為考慮化學(xué)的目的能夠被忽略。因此，顯著占據(jù)的NBOs的有效延伸減至NAOs的NMB部分，與化學(xué)知識一致。價基非路易斯NBOs{Ω*AB}被一系列"Rydberg-42價基非路易斯NBOs{Ω*AB}被一系列"Rydberg-

2.NBO程序介紹KeywordParms?KeywordDescriptionAOINFONWriteAObasisinformationtoLFN31ARCHIVEOWriteARCHIVE(FILE47)forstand-aloneGENNBOinputBNDIDXNNAO-WibergBondIndexandrelatedvalencyindicesFILEYSpecifyfilestemforPLOTfilesPLOTNWritefilesfororbitalplotting

3CBONDNSearchfor3-centerNBOs

ControlOptions2.NBO程序介紹KeywordPar432.NBO程序介紹KeywordParMainProgramOptions

KeywordParms?

KeywordDescription

Page

[BEND]O.Hybriddirectionalityand"bond-bending"analysisCMOO.BondingcharacterofcanonicalmolecularorbitalsDIPOLEO.Dipolemomentanalysis[E2PERT]O.2nd-orderperturbativeestimatesofNBOinteractionsNBBPO.Naturalbond-bondpolarizabilityindices[NBO]NNaturalbondorbitalcompositions[NBOSUM]N.NBOsummarytableNCSO.NaturalchemicalshieldinganalysisNJCO.NaturalJ-couplinganalysisNLMONNaturallocalizedmolecularorbitalcompositions[NPA]NNaturalpopulationanalysisNRTNNaturalresonancetheoryanalysisSTERICO.Naturalstericanalysis3CHBN3-c,4-ehyperbondsearchKeywordsinbracketsdenote[default]optionsthatareperformedevenifthe$NBOkeylistisempty.Notethatsomeoptionsautomaticallyturnonotherkeywordsthatareneededtoperformtheanalysis(e.g.,NLMOisautomaticallyturnedonforDIPOLE,NCS,orNJCanalysis).Usethevariouscontroloptionkeywords(suchasthePRINTorthresholdkeywords)tofurthercontroloutputfromeachmainprogramoption.

MainProgramOptionsKeywo44MainProgramOptionsKeywoNBOTranslatesAccurateCalculationsIntoChemicalInsightsChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…NBOTranslatesAccurateCalcul45NBOTranslatesAccurateCalculNaturalPopulationAnalysisChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…SummaryofNaturalPopulationAnalysis: NaturalPopulation NaturalAtom# ChargeCoreValenceRydbergTotalC1 -0.440791.999004.438480.003316.44079N2 -0.897151.999535.893780.003847.89715H3 0.183700.000000.814530.001770.81630H4 0.217130.000000.781920.000960.78287H5 0.217130.000000.781920.000960.78287H6 0.359990.000000.638790.001220.64001H7 0.359990.000000.638790.0012 0.64001=======================================================================*Total* 0.000003.9985313.988200.0132818.00000****SampleOutput****thenaturalpopulationsaresummarizedasaneffectivevalenceelectronconfiguration("naturalelectronconfiguration")foreachatom:Atom#NaturalElectronConfigurationC1[core]2s(1.09)2p(3.35)N2[core]2s(1.43)2p(4.47)H31s(0.81)H41s(0.78)H51s(0.78)H61s(0.64)H71s(0.64)NaturalPopulationAnalysisCha46NaturalPopulationAnalysisChaNATURALBONDORBITALS(Summary): PrincipalDelocalizationsNBO Occupancy Energy (geminal,vicinal,remote)=======================================================================Molecularunit1(CH3NO)1.BD(1)H1-N3 1.99309 -0.89250 32(v),20(v)2.BD(1)H2-N3 1.99322 -0.87920 3(v),19(v),32(v),21(v)3.BD(1)N3-C4 1.99828 -1.10527 29(g),28(g)4.BD(1)C4-O5 1.99925 -0.50592 31(g),16(v)5.BD(2)C4-O5 1.99802 -1.40674 19(g),28(v)6.BD(1)C4-H6 1.98929 -0.75792 29(v),23(v),15(v)7.CR(1)N3 1.99922 -15.31924 20(v),19(v),13(v),14(v)8.CR(1)C4 1.99939 -11.16963 27(v),29(v),28(v)9.CR(1)O5 1.99963 -20.09206 19(v),25(g),20(v)10.LP(1)N3 1.80683 -0.39458 31(v),22(v11.LP(1)O5 1.98262 -0.93620 19(v),20(v),33(v),30(v) 29(r)12.LP(2)O5 1.88568 -0.40982 30(v),33(v),20(v)****SampleOutput****NBOSummaryChargesLewisDiagramsBondTypesHybridDescriptorsBondOrdersChargeTransferNMRDescriptorsResonanceWeightsAndmore…NATURALBONDORBITALS(Summary47NATURALBONDORBITALS(Summary1.H1-N3?NBOType

N-Hsigmabond

?HybridComposition

0.5390(s)H+0.8423(sp2.23)N?Occupancy

1.99309

e

NaturalBondOrbitalAn