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Computational Chemistry: Reviews of Current Trends PDF

255 Pages·2002·10.527 MB·English
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Computational m o c c. ntifi e Chemistry ci s d orly. wnl ww.se o wu m al d froerson Reviews of Current Trends ep ador oF Downl3/14. urrent Trends RSITY on 09/0 Volume 7 CE s of NIV wU vieD eR RO stry: ANF miT Cheby S al n o ati ut p m o C Computational Chemistry: Reviews of Current Trends Editor-in-Charge: Jerzy Leszczynski, Dept. of Chemistry, Jackson State University, USA Published Vol. 1: Computational Chemistry: Reviews of Current Trends m o Edited by Jerzy Leszczynski c c. ntifi Vol. 2: Computational Chemistry: Reviews of Current Trends cie Edited by Jerzy Leszczynski s d orly. Vol. 3: Computational Chemistry: Reviews of Current Trends wnl ww.se o Edited by Jerzy Leszczynski wu m al Vol. 4: Computational Chemistry: Reviews of Current Trends d froerson Edited by Jerzy Leszczynski ep oadFor Vol. 5: Computational Chemistry: Reviews of Current Trends wnl4. Edited by Jerzy Leszczynski Do3/1 urrent Trends RSITY on 09/0 Vol. 6: CEodmitepdu tbayti oJnearzl yC Lheesmzicsztryyn: sRkei views of Current Trends CE s of NIV wU vieD eR RO stry: ANF miT Cheby S al n o ati ut p m o C Computational m o c c. Chemistry ntifi e ci s d orly. wnl ww.se o wu m al d froerson Reviews of Current Trends ep ador oF Downl3/14. urrent Trends RSITY on 09/0 Volume 7 CE s of NIV wU vieD eR RO stry: ANF miT Cheby S editor nal Jerzy Leszczynski o ati ut p m Department of Chemistry o C Jackson State University USA V fe World Scientific wb NNeeww J Jeerrsseeyy'S • iSnainagpaoproer*e •L Loonnddoonn* • Hong Kong Published by World Scientific Publishing Co. Pte. Ltd. P O Box 128, Fairer Road, Singapore 912805 USA office: Suite IB, 1060 Main Street, River Edge, NJ 07661 UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE m o c c. ntifi e ci s d worlnly. British Library Cataloguing-in-Publication Data ww.se o A catalogue record for this book is available from the British Library. wu m al d froerson ep ador oF Downl3/14. Current Trends ERSITY on 09/0 VCoOluMmPeU 7T ATIONAL CHEMISTRY: REVIEWS OF CURRENT TRENDS s of NIV Copyright © 2002 by World Scientific Publishing Co. Pte. Ltd. wU evieRD Aellel crtirgohntisc roers emrevcehda. nTihciasl ,b ionocklu, doirn pga prhtso ttohceorpeyoifn, gm, areyc noordt ibneg roerp arondy uicnefodr imna atnioyn f osrtomr aogre bayn da nrye tmrieeavnasl , RO stry: ANF system now known or to be invented, without written permission from the Publisher. miT Cheby S al n o utati For photocopying of material in this volume, please pay a copying fee through the Copyright mp Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to Co photocopy is not required from the publisher. ISBN 981-238-116-3 Printed in Singapore by Uto-Print PREFACE For the second time in 2001 Chemical & Engineering News (CEN) presented chemistry research highlights from the past year. The senior CEN correspondent Stu Borman selected the most important 86 research advances for this year. They are devided into eight categories: nanotech and molecular electronics, biochemistry, catalysis, genomics and medicine, organic chemistry, polymer m chemistry, physical chemistry, and sensors. o c c. In reading over these advances I have realized how crucial is the need for ntifi efficient computational performance not only in basic science, but also in almost e ci all areas of technological applications. New nano-scale devices developed for s d orly. Molecular Electronics could be easily the primary objects for such www.wuse onl comIpnu ttahteio nfiarsl tt ecchhanpitqeure so.f the Vllth volume of our book series M. Di Ventra d from ersonal rsetrvuecatluerse st haet dtheeta ialsto mofi c plreevdeicl.t ioSnusc ho fk ntohwe letrdagnes piosr to fp riompeprotrietasn coef imn osloeclvuilnagr ep ador crucial technological problems as electromigration or temperature and statistical oF Downl3/14. edfefveicctse.s , Ohof wmeavjeorr, ain bterrieesf t diiss ctuhses iocnu rroefn tt-hveo lrtoalgee ocfh caurarcretenrti-sintidcus ceodf mfoorcleecsu loanr urrent Trends RSITY on 09/0 mtahraoenl Aeq caulut ihfcleaokwrul ygw t hhgir oaecuisuns riiarnsne gand lt pslayooto pgrmueivlssate,rrn iinct.yo te ndaem mtoop nicrgaic lrcaeuls le(aaatirboc nhinsei rtosio f i)ns qyvusetasentmitgusam tcin ocgnh teavmianriiicnoagul s nm aoes tmpheoocdrtess CE s of NIV of biological systems. Contrary to Force Field (FF) methods, quantum chemical wU methods do not require empirical parameters and do produce results of evieRD experimental accuracy. Moreover, quantum chemical methods allow molecular RO mistry: TANF strucTthuere sin aitnidal p aropppelirctiaetiso tno boef satbud iineidt isoi mmueltthaondeos uassly a. means of calibrating FF Cheby S parameters for Molecular Dynamics calculations has been superseded by al nonempirical investigations of complex DNA fragments. The number and n atio significance of such studies will certainly increase in the near future. ut The development of efficient methods for application to large molecular p m o systems is a focus of two chapters. C. F. Guerra, F. M. Bickelhaupt and E. J. C Baerends present an overview of development and applications of parallel and order-N Density Functional Theory (DFT) methods. The approaches developed in this research group allow one to address important issues concerning structures and energetics of the DNA segments. The next review written by S. Saebo addresses development of new methods for calculations of electron dynamical correlation for large molecular systems. In order to study large molecules using advanced ab initio approaches the steep vi Preface power-law scaling has to be reduced. It could be achieved through reformulation of correlation methods using localized canonical orbitals. This chapter mainly concentrates on progress in the development of the least expensive second order Moller-Plessett (MP2) electron correlation methods, however, more accurate approaches are also discussed. For small and medium sized molecules, the chemical accuracy of quantum chemical predictions has been already achieved in many fields of applications. Among the most accurate methods are Coupled Cluster (CC) approaches. Their m o accuracy comes at price - such methodologies are among the most c ntific. cfroommp uthtaet iCoCna alyp pdroemacahnedsi,n tgh em coetnhnoedcste. dI ntr ioprldee erx ctoit aotibotnasin ( Tq)u haanvtieta ttoiv bee ainccculurdaceyd e sci in the calculation scheme. J. D. Watts reviews different approximate strategies d orly. developed to include triple excitations within the coupled cluster methods. His wnl ww.se o chapter provides clear descriptions of the approximations used and discusses wu their performance and accuracy. In addition, the provided results allow one to m al d froerson aenstda bPli.s hV tahleir olinm irtes voefa ltsh ea CnoCtSheDrT a mspeetchto do.f Tthhee nCexCt cchaalcputelar twiornistt.e nT hbey Ja.u Nthoogras ep ador discuss the performance of the explicitly correlated CC method based on the so oF Downl3/14. cadaldlereds sRe1d2. Iann saadtzd.i tTiohne, ptrhoeb lcehmap otefr b aaslsiso spertosv siudietsa belex afmorp ltehse Rof1 2c aclcaulcluatliaotinosn sf oisr urrent Trends RSITY on 09/0 helyedcrTtorhogene incQ ausntadrnu ctcuatmrubr oeM nc. oallceuculaltairo nDs yfnoarm micosl e(cQuMlarD r)e aacptpioronasc. hF ohra ss mraelvlo mluotiloenciuzleeds CE such studies have augmented experimental investigations of reaction s of NIV intermediates and mechanisms. QMD is of tremendous interest in providing viewD U details of atmospheric reactions. ReOR The last chapter of the volume, contributed by Y. Ishikawa and R.C. stry: ANF Binning, Jr. provides details of their QMD studies on interconversion of miT nitronium ion and nitric acid in small water clusters. The ab initio direct Cheby S molecular dynamics simulations provided comprehensive understanding of the al title reactions. The obtained data are crucial in understanding of an outcome of n o ati experimental studies on cluster fragmentation. ut p I would like to thank all the authors for the excellent contributions and m o fruitful collaboration. The very efficient technical assistance of Dr. Manoj K. C Shukla in putting together this volume is greatly appreciated. As always, your feedback is very important to me, please feel free to e-mail your suggestions to [email protected]. Jerzy Leszczynski Jackson, MS, November 2001 CONTENTS Preface v 1. Molecules as Components in Electronic Devices: A First-Principles Study 1 m Massimiliano Di Ventra o c c. ntifi 2. Tackling DNA with Density Functional Theory: Development and e ci Application of Parallel and Order-N DFT Methods 17 s d orly. Celia Fonseca Guerra, F. Matthias Bickelhaupt, wnl Evert Jan Baerends and Jaap G. Snijders ww.se o wu d from ersonal 3. LoSwv-eSinc alSinage bM0 ethods for Electron Correlation 63 ep ador oF Downl3/14. 4. Iinte rCaotiuvpel eadn-dC lNuostne-rI tMeraettihvoed sI.n cTluhseioorny oafn Cd oNnunmecetreidc aTl riCpolem Epaxrciistoantiso ns urrent Trends RSITY on 09/0 forJ oShonm De .D iWffiactutslt Examples 89 CE 5. Explicitly Correlated Coupled Cluster R12 Calculations 131 s of NIV Jozef Noga and Pierre Valiron wU vieD eR RO 6. Ab Initio Direct Molecular Dynamics Studies of Atmospheric stry: ANF Reactions: Interconversion of Nitronium Ion and Nitric Acid miT in Small Clusters 187 Cheby S Yasuyuki Ishikawa and R. C. Binning, Jr. al n o ati Index 245 ut p m o C Chapter 1: Molecules as Components in Electronic Devices: A First-Principles Study Massimiliano Di Ventra Department of Physics m co Virginia Polytechnic Institute and State University c. ntifi Blacksburg, VA, 24061, USA e ci s d orly. wnl ww.se o wu m al Introduction ed froperson Thanks in large part to the ever-increasing need for computational oadFor performance in nearly every technological application, and the approaching Current Trends DownlERSITY on 09/03/14. pmpaecllehhetiriyeccfprrsot,noir rcoaempantlihle iv ccyfleu tis mrniodccineitts iivroctioinssnca, . es td[ hsc1m ieh]d aweenIpmntuis ttmih hisc atbassenl t raobao n oenro cfda -o tsnrmtceaoaanlendolg saegiciy nsol teeudoaesirrrm s sst t oeethh mhnataashtit ivco owceosna enesn dd.o niubfrec Teeett chhoditnee re t-sdaetbe r g aantrsnehdaeswetedieivs ,rd ti g oceiaernn,ts ttse oeaor nnhalatdiat idi voso-oiensnnt t hgaoettltooeerf s of NIV key components of today microcircuits, and have to outperform, by orders of wU magnitude, the integration level of today's chips at a manufacturing cost evieRD comparable to the present technology. A field that has grown around these RO mistry: TANF pimremmeinsesse liys kpnoowwenrf uasl Mcoolmecpuultairn gE lceicrtcruointisc sb. aTsehde uonnd etrrliylliinogn si deoaf isi ntdoi vcirdeuatael Cheby S building blocks, each no larger than a single molecule. Though the idea has al been around for more than two decades, [2] only recently measurements of n o current-voltage characteristics of individual molecules have been feasible. utati [3-5] In order to further develop this new technology, however, a more p m fundamental understanding of the transport properties of molecular o C structures at the atomic level is required. This will be essential in solving important technological problems such as electromigration, temperature and l 2 Massimilia.no Di Ventra statistical effects that have already been major concerns in the present microelectronics. Theory can provide invaluable help like it did in the past for conventional electronics to achieve the goals of our society. In particular, first-principles approaches that have had an enourmous impact in Physics, Chemistry and Materials Science can play an equally important role in the development of these new technologies. In this Chapter, I will review recent work on first-principles calculations of current-voltage (I-V) characteristics of molecular devices for m o which experimental data are available. In particular, I will outline the c c. theoretical method used in such calculations and its application to two- and ntifi three-terminal device configurations. Also, I will briefly discuss the role of e sci current-induced forces on molecular wires and their role in weakening d orly. chemical bonds at the contacts and in the wire. wnl ww.se o wu m al d froerson Transport in Nanoscale Conductors from First Principles ep oadFor Semiempirical methods for the calculation of current in small structures Current Trends DownlERSITY on 09/03/14. pmtes1huxl0aoeca]c lcm eemeFcdpsouos lrbfell euee,ic sltnt wuhsatlteeonea es dnrnp o cnar letoenaw, v ndosoio edfa t mmeuct buietaeerhtm raseue.l pn s e[ecit6r-lfoeiiu-ncn1clatd t0arlua]co c cttdiOsecge odhnsiu s t fh-nt ohbaatr ievncno ee dofi stib m hnteohegperer on m nrh ltodiaaonnenndev-dteale i,lrln iso sce tsphhraueaaarendrv g es etfoep ofv boe reecreutretdn s ntip.dhs retIreorren ispmyb tteaeuharnatitririsdkoes ,acn.s ba [ f6olsioyne-fr s of NIV a set of first-principles methods is necessary. viewD U The example in Fig. 1 is a schematic of a typical system eR investigated. It consists of a molecule (or equivalently any set of atoms) RO mistry: TANF bTehtew eseanm ptwleo ibsu plka ret leocft raond eesx wtehrnicahl acrierc kueitp tw aht icah c,e ritna ifni rpsto taepnptiraol xdimiffaetrioennc eis. Cheby S assumed to have zero impedence. Electrons are assumed to travel (say) from al the right electrode without scattering until they reach a region in space close n atio to the sample region (the molecule). Since the details of the electrodes are ut not important up to the interface with the sample, we represent them using a p m uniform-background (jellium) model. [11] The interface atoms and the o C sample atoms are represented within a pseudopotential framework. The transport properties of the sample will be computed by means of the Lippmann-Schwinger equation following Lang's approach. [11] Initially one calculates single-particle wavefunctions and self-consistent electron Molecules as Components in Electronic Devices: A First-Principles Study 3 /-*> n D -•"-» m o c ntific. Fatiogmurse. 1: Schematic of a benzene molecule connected to gold electrodes via sulfur e ci s d orly. wnl www.use o dweinthsiinti eas dfoenr stihtye bfuanrect imoneatal llfiocr melaelcitsrmod. e[s1 1in] tThhee pnr, etsheen cLei popfm thaen nb-iSacsh vwoilntaggeer d from ersonal aenqdua toionne- eisle csotrlovne dw toav oeb tfauinnc ttihoen ss teiand yth-set atwe hsoellef- csoynssteismte,n tc oenlesicsttrionng doefn stihtye ep ador sample and the electrodes, which are maintained at distinct values of the oF Downl3/14. eSlcehcwtroinsgtaetri ce qpuoatetinotnia tlo c boerr esosplvoendd iins:g to the external voltages. The Lippmann- urrent Trends RSITY on 09/0 VMA(r) =>FM(r) + f d\,d3r"GM(r,r,)SV(r'r")VMA(r"), (1) CE where MA and M refer to the complete system and to the pair of bare biased ws of UNIV metal electrodes, respectively.[l] G is the Green's function of the bare vieD biased metal electrodes and 5 V is eR RO Chemistry: by STANF oV(r,r') = vps{r,r) +[vxc(nMA(r)) -vxc(nM(r)) + j d3r"&n(r"))/\r-r'\] 5(r- r')(2) nal The term v (r,r ) is the sum of the nonlocal pseudopotentials representing o ps utati the atomic cores, v c(nMA(r)) is the exchange correlation functional that p X m o C

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